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
Unknown	0	broad.mit.edu	37	1	13634735	13634735	+	RNA	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13634735C>T	uc001auz.3	+	4		c.948C>T								Homo sapiens PRAME family member 10, mRNA (cDNA clone MGC:138413 IMAGE:8327676), complete cds.																		CTCAAGAACCCCTTGGGGGCC	0.502													4	28	---	---	---	---	PASS
KPNA6	23633	broad.mit.edu	37	1	32631815	32631815	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32631815A>G	uc001bug.2	+	11	1188	c.1100A>G	c.(1099-1101)AAC>AGC	p.N367S	KPNA6_uc001buh.2_Missense_Mutation_p.N142S|KPNA6_uc010ogx.1_Missense_Mutation_p.N364S|KPNA6_uc010ogy.1_Missense_Mutation_p.N372S|KPNA6_uc009vtz.2_Missense_Mutation_p.N262S	NM_012316	NP_036448	O60684	IMA7_HUMAN	karyopherin alpha 6	367	NLS binding site (minor) (By similarity).|ARM 7.				NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				ACTGCTGGCAACAGGGCTCAA	0.463													9	368	---	---	---	---	PASS
STIL	6491	broad.mit.edu	37	1	47717395	47717395	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47717395A>T	uc001crc.1	-	17	3432	c.3277T>A	c.(3277-3279)TTC>ATC	p.F1093I	TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Missense_Mutation_p.F1047I|STIL_uc010omo.1_Missense_Mutation_p.F1076I|STIL_uc001crd.1_Missense_Mutation_p.F1094I|STIL_uc001cre.1_Missense_Mutation_p.F1093I	NM_003035	NP_003026	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 2	1093					cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				AGAAGGCTGAATGGGTCACAA	0.363													82	156	---	---	---	---	PASS
ADORA3	140	broad.mit.edu	37	1	112042773	112042773	+	Silent	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112042773G>A	uc001ebh.3	-	2	1523	c.756C>T	c.(754-756)ATC>ATT	p.I252I	ADORA3_uc001ebg.3_Intron|ADORA3_uc001ebf.2_Intron	NM_000677	NP_000668	P33765	AA3R_HUMAN	adenosine A3 receptor isoform 2	252	Helical; Name=6; (By similarity).				activation of adenylate cyclase activity|inflammatory response|regulation of heart contraction	integral to plasma membrane	adenosine receptor activity, G-protein coupled			ovary(2)|large_intestine(1)|skin(1)	4		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)	TAAAGTAGATGATGCAGTTGA	0.448													52	120	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145299738	145299738	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145299738C>T	uc001end.3	+	6	822	c.787C>T	c.(787-789)CCC>TCC	p.P263S	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.P263S|NBPF10_uc010oyi.1_5'Flank|NBPF10_uc001emq.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	263											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AGTCCCTGGCCCCACCTCTTC	0.493													4	90	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152277657	152277657	+	Silent	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152277657A>G	uc001ezu.1	-	3	9741	c.9705T>C	c.(9703-9705)GCT>GCC	p.A3235A		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3235	Ser-rich.				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)			GGTTTCTGGAAGCAGACCCAG	0.597									Ichthyosis				57	145	---	---	---	---	PASS
LMNA	4000	broad.mit.edu	37	1	156105094	156105094	+	Silent	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156105094C>G	uc001fni.2	+	5	1176	c.927C>G	c.(925-927)CTC>CTG	p.L309L	LMNA_uc001fnf.1_Silent_p.L309L|LMNA_uc001fng.2_Silent_p.L309L|LMNA_uc001fnh.2_Silent_p.L309L|LMNA_uc009wro.1_Silent_p.L309L|LMNA_uc010pgz.1_Silent_p.L197L|LMNA_uc001fnj.2_Silent_p.L228L|LMNA_uc001fnk.2_Silent_p.L210L|LMNA_uc009wrp.2_Missense_Mutation_p.S37C|LMNA_uc010pha.1_5'Flank	NM_170707	NP_733821	P02545	LMNA_HUMAN	lamin A/C isoform 1 precursor	309	Coil 2.|Rod.				cellular component disassembly involved in apoptosis|cellular response to hypoxia|establishment or maintenance of microtubule cytoskeleton polarity|muscle organ development|positive regulation of cell aging|regulation of apoptosis|regulation of cell migration	cytoplasm|lamin filament|nuclear envelope|nuclear envelope|perinuclear region of cytoplasm	protein binding|structural molecule activity|structural molecule activity			ovary(2)	2	Hepatocellular(266;0.158)					TCAGCCAGCTCCAGAAGCAGG	0.572									Werner_syndrome|Hutchinson-Gilford_Progeria_Syndrome				4	10	---	---	---	---	PASS
FCRL2	79368	broad.mit.edu	37	1	157739752	157739752	+	Missense_Mutation	SNP	C	T	T	rs138011295		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157739752C>T	uc001fre.2	-	4	558	c.499G>A	c.(499-501)GTG>ATG	p.V167M	FCRL2_uc001frd.2_5'Flank|FCRL2_uc010phz.1_Missense_Mutation_p.V167M|FCRL2_uc009wsp.2_Intron|FCRL2_uc010pia.1_Missense_Mutation_p.V167M	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor	167	Extracellular (Potential).|Ig-like C2-type 2.				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TCACTCCACACGGCAGAAATC	0.532													8	85	---	---	---	---	PASS
TGFB2	7042	broad.mit.edu	37	1	218609363	218609363	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218609363C>T	uc001hlm.2	+	5	1459	c.806C>T	c.(805-807)TCC>TTC	p.S269F	TGFB2_uc001hln.2_Missense_Mutation_p.S297F|TGFB2_uc010pue.1_Intron|TGFB2_uc001hlo.2_Intron	NM_003238	NP_003229	P61812	TGFB2_HUMAN	transforming growth factor, beta 2 isoform 2	269					activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway	axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen	beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding				0				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		ACTATAAAGTCCACTAGGAAA	0.423													60	143	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228528242	228528242	+	Silent	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228528242C>T	uc009xez.1	+	71	17495	c.17451C>T	c.(17449-17451)CCC>CCT	p.P5817P	OBSCN_uc001hsn.2_Silent_p.P5817P|OBSCN_uc001hsr.1_Silent_p.P446P	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	5817	DH.				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)				CAGGGGACCCCTCTCAGCCCC	0.657													10	14	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	905820	905820	+	5'Flank	SNP	T	A	A	rs13403700		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:905820T>A	uc010ewg.2	-						uc010ewh.1_Missense_Mutation_p.E42D					Homo sapiens cDNA FLJ46162 fis, clone TESTI4002520.																		GGTGTTTCATTTCCTCCCGGC	0.622													5	69	---	---	---	---	PASS
C2orf71	388939	broad.mit.edu	37	2	29295855	29295855	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29295855G>A	uc002rmt.1	-	1	1273	c.1273C>T	c.(1273-1275)CGA>TGA	p.R425*		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	425					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1						TCCTGTGCTCGTGGCTGAACC	0.572													40	86	---	---	---	---	PASS
CCDC88A	55704	broad.mit.edu	37	2	55591117	55591117	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55591117G>C	uc002ryv.2	-	6	1297	c.455C>G	c.(454-456)ACA>AGA	p.T152R	CCDC88A_uc010yoz.1_Missense_Mutation_p.T152R|CCDC88A_uc010ypa.1_Missense_Mutation_p.T152R|CCDC88A_uc010ypb.1_Missense_Mutation_p.T54R	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	152					activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						CGCTGCTTTTGTATCAAAATC	0.303													10	269	---	---	---	---	PASS
ACTR2	10097	broad.mit.edu	37	2	65488448	65488448	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65488448C>T	uc002sdq.2	+	7	1018	c.803C>T	c.(802-804)CCT>CTT	p.P268L	ACTR2_uc010yqf.1_Missense_Mutation_p.P213L|ACTR2_uc002sdp.2_Missense_Mutation_p.P273L|ACTR2_uc010yqg.1_Missense_Mutation_p.P216L	NM_005722	NP_005713	P61160	ARP2_HUMAN	actin-related protein 2 isoform b	268					cellular component movement	Arp2/3 protein complex|cell projection|cytoplasm	actin binding|ATP binding				0						TTATTTCAGCCTCACTTGATC	0.413													135	337	---	---	---	---	PASS
PNO1	56902	broad.mit.edu	37	2	68401898	68401898	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68401898T>G	uc002seh.2	+	7	785	c.723T>G	c.(721-723)ATT>ATG	p.I241M		NM_020143	NP_064528	Q9NRX1	PNO1_HUMAN	partner of NOB1	241						nucleolus	RNA binding				0						ATGGCAATATTCGAGCTGTGG	0.368													134	280	---	---	---	---	PASS
CNRIP1	25927	broad.mit.edu	37	2	68520911	68520911	+	3'UTR	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68520911C>A	uc002sek.3	-	3					CNRIP1_uc002sej.3_Intron|CNRIP1_uc002sem.1_RNA|CNRIP1_uc002sel.3_RNA	NM_015463	NP_056278	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1								protein binding			liver(1)	1						AATGGTGTGGCATGCCTTGTT	0.433													4	21	---	---	---	---	PASS
DYSF	8291	broad.mit.edu	37	2	71896302	71896302	+	Silent	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71896302C>A	uc002sie.2	+	49	5866	c.5490C>A	c.(5488-5490)CTC>CTA	p.L1830L	DYSF_uc010feg.2_Silent_p.L1861L|DYSF_uc010feh.2_Silent_p.L1837L|DYSF_uc002sig.3_Silent_p.L1816L|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Silent_p.L1851L|DYSF_uc010fef.2_Silent_p.L1868L|DYSF_uc010fei.2_Silent_p.L1847L|DYSF_uc010fek.2_Silent_p.L1848L|DYSF_uc010fej.2_Silent_p.L1838L|DYSF_uc010fel.2_Silent_p.L1817L|DYSF_uc010feo.2_Silent_p.L1862L|DYSF_uc010fem.2_Silent_p.L1852L|DYSF_uc010fen.2_Silent_p.L1869L|DYSF_uc002sif.2_Silent_p.L1831L|DYSF_uc010yqy.1_Silent_p.L711L|DYSF_uc010yqz.1_Silent_p.L591L	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1830	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						ACCTGAGCCTCACGGGGGAGA	0.527													57	80	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141806678	141806678	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141806678C>T	uc002tvj.1	-	11	2638	c.1666G>A	c.(1666-1668)GTA>ATA	p.V556I	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	556	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CGAGGGTTTACCAGATTTTCT	0.433										TSP Lung(27;0.18)			36	337	---	---	---	---	PASS
ORMDL1	94101	broad.mit.edu	37	2	190640204	190640204	+	Intron	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190640204A>G	uc002urb.3	-						ORMDL1_uc002urc.3_Intron|ORMDL1_uc002urd.3_Intron|ORMDL1_uc002ure.3_Intron|ORMDL1_uc002urf.3_3'UTR	NM_016467	NP_057551	Q9P0S3	ORML1_HUMAN	ORM1-like 1						ceramide metabolic process	endoplasmic reticulum membrane|integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(117;0.00177)|Epithelial(96;0.0317)|all cancers(119;0.0889)			TTGCAACAAAATATGTTTCTA	0.294													10	54	---	---	---	---	PASS
NIF3L1	60491	broad.mit.edu	37	2	201761932	201761932	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201761932C>A	uc002uwm.2	+	5	951	c.860C>A	c.(859-861)ACC>AAC	p.T287N	NIF3L1_uc002uwl.2_Missense_Mutation_p.T260N|NIF3L1_uc002uwn.2_Missense_Mutation_p.T260N|NIF3L1_uc002uwo.2_Missense_Mutation_p.T287N|NIF3L1_uc002uwp.2_Missense_Mutation_p.T287N|NIF3L1_uc002uwq.2_Intron	NM_001136039	NP_001129511	Q9GZT8	NIF3L_HUMAN	NIF3 NGG1 interacting factor 3-like 1 isoform 1	287					positive regulation of transcription, DNA-dependent		transcription factor binding			skin(1)	1						GTGGGGAGAACCTTAGGTAAA	0.403													61	125	---	---	---	---	PASS
ABCA12	26154	broad.mit.edu	37	2	215846952	215846952	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215846952G>A	uc002vew.2	-	30	4758	c.4538C>T	c.(4537-4539)TCT>TTT	p.S1513F	ABCA12_uc002vev.2_Missense_Mutation_p.S1195F|ABCA12_uc010zjn.1_Missense_Mutation_p.S440F	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1513	ABC transporter 1.				cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ACTTCGGCGAGAACATGGGTC	0.428													8	276	---	---	---	---	PASS
USP37	57695	broad.mit.edu	37	2	219423354	219423354	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219423354C>A	uc002vie.2	-	4	476	c.23G>T	c.(22-24)GGT>GTT	p.G8V	USP37_uc010fvs.1_Missense_Mutation_p.G8V|USP37_uc010zkf.1_Missense_Mutation_p.G8V|USP37_uc002vif.2_Missense_Mutation_p.G8V|USP37_uc002vig.2_Intron|USP37_uc010zkg.1_Missense_Mutation_p.G8V	NM_020935	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	8					ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TCTGATAGGACCATGTATCTT	0.343													114	318	---	---	---	---	PASS
TRIP12	9320	broad.mit.edu	37	2	230670506	230670506	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230670506C>A	uc002vpw.1	-	17	2474	c.2365G>T	c.(2365-2367)GAC>TAC	p.D789Y	TRIP12_uc002vpx.1_Missense_Mutation_p.D837Y|TRIP12_uc002vpy.1_Missense_Mutation_p.D519Y|TRIP12_uc010zlz.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	789	WWE.				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)		GTTCCCGTGTCCTCATTGATT	0.423													26	477	---	---	---	---	PASS
SETD5	55209	broad.mit.edu	37	3	9486834	9486834	+	Silent	SNP	A	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9486834A>C	uc003brt.2	+	12	1725	c.1290A>C	c.(1288-1290)CCA>CCC	p.P430P	SETD5_uc003brs.1_Silent_p.P411P|SETD5_uc003bru.2_Silent_p.P332P|SETD5_uc003brv.2_Silent_p.P319P|SETD5_uc010hck.2_5'UTR|SETD5_uc003brw.1_Silent_p.P99P|SETD5_uc003brx.2_Silent_p.P99P	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	430										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		CACCTCCTCCAAGCCTACCCA	0.473													95	67	---	---	---	---	PASS
CELSR3	1951	broad.mit.edu	37	3	48682639	48682639	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48682639C>G	uc003cul.2	-	25	8082	c.7801G>C	c.(7801-7803)GTG>CTG	p.V2601L	CELSR3_uc003cuf.1_Missense_Mutation_p.V2698L|CELSR3_uc010hkf.2_5'Flank|CELSR3_uc010hkg.2_Missense_Mutation_p.V584L	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	2601	Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GCAGTGCACACCAGCTGAGGG	0.627													5	9	---	---	---	---	PASS
MON1A	84315	broad.mit.edu	37	3	49948281	49948281	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49948281A>T	uc003cxz.2	-	4	1067	c.941T>A	c.(940-942)CTG>CAG	p.L314Q	MON1A_uc003cya.2_Missense_Mutation_p.L152Q|MON1A_uc003cyb.2_Missense_Mutation_p.L152Q	NM_032355	NP_115731	Q86VX9	MON1A_HUMAN	MON1 homolog A isoform a	217							protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		CACTAGCACCAGCGGGCTCCG	0.607													2	1	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52651513	52651513	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52651513T>A	uc003des.2	-	14	1595	c.1583A>T	c.(1582-1584)AAT>ATT	p.N528I	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.N528I|PBRM1_uc003der.2_Missense_Mutation_p.N496I|PBRM1_uc003det.2_Missense_Mutation_p.N543I|PBRM1_uc003deu.2_Missense_Mutation_p.N543I|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.N528I|PBRM1_uc010hmk.1_Missense_Mutation_p.N528I|PBRM1_uc003dey.2_Missense_Mutation_p.N528I|PBRM1_uc003dez.1_Missense_Mutation_p.N528I|PBRM1_uc003dfb.1_Missense_Mutation_p.N441I|PBRM1_uc003dfc.2_5'Flank	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	528					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)		AAGAACAACATTGAATAAGAT	0.348			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								79	71	---	---	---	---	PASS
ITIH4	3700	broad.mit.edu	37	3	52858241	52858241	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52858241A>T	uc003dfz.2	-	9	1172	c.1136T>A	c.(1135-1137)CTC>CAC	p.L379H	ITIH4_uc011bel.1_Missense_Mutation_p.L109H|ITIH4_uc003dfy.2_Missense_Mutation_p.L243H|ITIH4_uc011bem.1_Missense_Mutation_p.L379H|ITIH4_uc011ben.1_Missense_Mutation_p.L379H	NM_002218	NP_002209	Q14624	ITIH4_HUMAN	inter-alpha (globulin) inhibitor H4	379	VWFA.				acute-phase response|hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CAGGATGATGAGTGAGACACT	0.632													8	7	---	---	---	---	PASS
SGEF	26084	broad.mit.edu	37	3	153909099	153909099	+	Silent	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153909099G>A	uc011bog.1	+	8	1873	c.1662G>A	c.(1660-1662)AAG>AAA	p.K554K	SGEF_uc011boh.1_Silent_p.K554K	NM_015595	NP_056410	Q96DR7	ARHGQ_HUMAN	Src homology 3 domain-containing guanine	554	DH.				regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CATCCTTTAAGGAAGTATTGT	0.408													26	560	---	---	---	---	PASS
YEATS2	55689	broad.mit.edu	37	3	183490251	183490251	+	Silent	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183490251G>C	uc003fly.2	+	16	2301	c.2106G>C	c.(2104-2106)GTG>GTC	p.V702V		NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	702					histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			AAGCAATTGTGAGTGGAGGTG	0.547													47	106	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505836	195505836	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505836G>C	uc011bto.1	-	3	12691	c.12231C>G	c.(12229-12231)CAC>CAG	p.H4077Q	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|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	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	0.597													19	41	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195508903	195508903	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195508903G>A	uc011bto.1	-	3	9624	c.9164C>T	c.(9163-9165)ACG>ATG	p.T3055M	MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|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)		AGGAAGAGGCGTGGTGTCACC	0.592													9	29	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195509171	195509171	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195509171G>A	uc011bto.1	-	3	9356	c.8896C>T	c.(8896-8898)CTT>TTT	p.L2966F	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)		ACTGAGGAAAGGCTGGTGACA	0.602													6	136	---	---	---	---	PASS
TMEM129	92305	broad.mit.edu	37	4	1719303	1719303	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1719303G>C	uc003gdn.2	-	3	1300	c.780C>G	c.(778-780)TTC>TTG	p.F260L	TMEM129_uc010iby.2_RNA|TMEM129_uc003gdm.2_Intron	NM_001127266	NP_001120738	A0AVI4	TM129_HUMAN	transmembrane protein 129 isoform a	260	Extracellular (Potential).					integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(23;0.00765)			ATGTCTCCAGGAACAGGTCGC	0.672													16	19	---	---	---	---	PASS
DTHD1	401124	broad.mit.edu	37	4	36345346	36345346	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36345346G>A	uc011bxy.1	+	9	2142	c.1751G>A	c.(1750-1752)CGC>CAC	p.R584H	DTHD1_uc003gsv.2_RNA	NM_001136536	NP_001130008	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	749	Death.			R -> S (in Ref. 1; BAG65199/BAH14894).	signal transduction						0						CGACATCTCCGCAAGATTGGC	0.458													31	40	---	---	---	---	PASS
CCNG2	901	broad.mit.edu	37	4	78085544	78085544	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78085544C>T	uc003hkq.3	+	7	1126	c.823C>T	c.(823-825)CGC>TGC	p.R275C	CCNG2_uc003hkn.3_Missense_Mutation_p.R275C|CCNG2_uc011ccc.1_Missense_Mutation_p.R275C|CCNG2_uc003hkp.3_Missense_Mutation_p.R275C	NM_004354	NP_004345	Q16589	CCNG2_HUMAN	cyclin G2	275					cell cycle checkpoint|cell division|mitosis	cytoplasm				ovary(2)|lung(1)	3						CGTTTCAAGGCGCACAGCCCA	0.468													53	109	---	---	---	---	PASS
DSPP	1834	broad.mit.edu	37	4	88536917	88536917	+	Missense_Mutation	SNP	G	A	A	rs143717970	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88536917G>A	uc003hqu.2	+	5	3223	c.3103G>A	c.(3103-3105)GAT>AAT	p.D1035N		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein preproprotein	1035	Asp/Ser-rich.				biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent			central_nervous_system(1)	1		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacagcagcgatagcagtga	0.000													6	23	---	---	---	---	PASS
DSPP	1834	broad.mit.edu	37	4	88536919	88536919	+	Silent	SNP	T	C	C	rs147223434	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88536919T>C	uc003hqu.2	+	5	3225	c.3105T>C	c.(3103-3105)GAT>GAC	p.D1035D		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein preproprotein	1035	Asp/Ser-rich.				biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent			central_nervous_system(1)	1		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgatagcagtgaca	0.000													8	24	---	---	---	---	PASS
TRAM1L1	133022	broad.mit.edu	37	4	118005673	118005673	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118005673C>A	uc003ibv.3	-	1	1064	c.877G>T	c.(877-879)GTG>TTG	p.V293L		NM_152402	NP_689615	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like	293	Lumenal (Potential).|TLC.				protein transport|transmembrane transport	endoplasmic reticulum membrane|integral to membrane				central_nervous_system(1)	1						GCTGCCAACACATTTACATTT	0.458													18	117	---	---	---	---	PASS
ZNF827	152485	broad.mit.edu	37	4	146824030	146824030	+	Silent	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146824030C>T	uc003ikn.2	-	2	429	c.381G>A	c.(379-381)CTG>CTA	p.L127L	ZNF827_uc003ikm.2_Silent_p.L127L|ZNF827_uc010iox.2_Intron	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827	127					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)					AACCAGCCTCCAGCAGCCGCC	0.582													4	17	---	---	---	---	PASS
FGG	2266	broad.mit.edu	37	4	155530781	155530781	+	Splice_Site	SNP	C	T	T	rs113700069		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155530781C>T	uc003ioj.2	-	6	807	c.666_splice	c.e6+1	p.K222_splice	FGG_uc003iog.2_Splice_Site_p.K222_splice|FGG_uc003ioh.2_Splice_Site_p.K230_splice|FGG_uc010ipx.2_Splice_Site_p.K50_splice|FGG_uc010ipy.2_Splice_Site|FGG_uc003ioi.2_Intron|FGG_uc003iok.2_Splice_Site_p.K230_splice	NM_021870	NP_068656	P02679	FIBG_HUMAN	fibrinogen, gamma chain isoform gamma-B						platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding				0	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	GAAAAAATTACCTTCTGAAAC	0.279													6	138	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	256592	256592	+	3'UTR	SNP	T	C	C	rs113703363		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:256592T>C	uc003jao.3	+	15					SDHA_uc011clw.1_3'UTR|SDHA_uc003jap.3_3'UTR|SDHA_uc003jaq.3_3'UTR|SDHA_uc003jar.3_3'UTR	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	TAATAGCTCATGCATGTGTCC	0.488									Familial_Paragangliomas				5	36	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	256624	256624	+	3'UTR	SNP	G	A	A	rs79810985	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:256624G>A	uc003jao.3	+	15					SDHA_uc011clw.1_3'UTR|SDHA_uc003jap.3_3'UTR|SDHA_uc003jaq.3_3'UTR|SDHA_uc003jar.3_3'UTR	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	GTCTTCATACGCTTCTGCACT	0.488									Familial_Paragangliomas				5	23	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469440	75469440	+	Intron	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469440A>G	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CAGAGCTACAATGCATTTAGT	0.418													7	251	---	---	---	---	PASS
IQGAP2	10788	broad.mit.edu	37	5	75886273	75886273	+	Silent	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75886273A>G	uc003kek.2	+	8	903	c.681A>G	c.(679-681)AAA>AAG	p.K227K		NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	227					small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		CAGTTGAAAAAGGAATAGCAG	0.378													77	155	---	---	---	---	PASS
CCNH	902	broad.mit.edu	37	5	86695281	86695281	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86695281C>A	uc003kjb.2	-	7	1034	c.802G>T	c.(802-804)GAA>TAA	p.E268*	CCNH_uc003kiy.1_RNA|CCNH_uc003kiz.1_Nonsense_Mutation_p.E215*|CCNH_uc003kja.2_Nonsense_Mutation_p.E215*	NM_001239	NP_001230	P51946	CCNH_HUMAN	cyclin H	268					G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cyclin-dependent protein kinase activating kinase holoenzyme complex|holo TFIIH complex	protein kinase binding			ovary(2)|kidney(1)	3		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;9.01e-39)|Epithelial(54;5.08e-33)|all cancers(79;4.28e-28)		GCAACTTCTTCAGATCTGGGT	0.368								Direct_reversal_of_damage|NER					102	221	---	---	---	---	PASS
SLC27A6	28965	broad.mit.edu	37	5	128321007	128321007	+	Silent	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128321007C>T	uc003kuy.2	+	3	1059	c.663C>T	c.(661-663)TAC>TAT	p.Y221Y	SLC27A6_uc003kuz.2_Silent_p.Y221Y	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	221	AMP (Potential).				long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		CTTGTCTTTACATTTTTACCT	0.418													37	90	---	---	---	---	PASS
SLC23A1	9963	broad.mit.edu	37	5	138713670	138713670	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138713670T>G	uc003leh.2	-	12	1544	c.1447A>C	c.(1447-1449)AAT>CAT	p.N483H	SLC23A1_uc003leg.2_Missense_Mutation_p.N487H	NM_005847	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (nucleobase	483					brain development|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|response to toxin|transepithelial L-ascorbic acid transport|water-soluble vitamin metabolic process	apical plasma membrane|cytoplasm|integral to plasma membrane|intracellular organelle|membrane fraction	dehydroascorbic acid transporter activity|L-ascorbate:sodium symporter activity|nucleobase transmembrane transporter activity|protein binding|sodium-dependent L-ascorbate transmembrane transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	GCACCTGTATTGATGGCGCCA	0.562													20	51	---	---	---	---	PASS
PCDHB6	56130	broad.mit.edu	37	5	140531176	140531176	+	Silent	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140531176C>T	uc003lir.2	+	1	1338	c.1338C>T	c.(1336-1338)GTC>GTT	p.V446V	PCDHB6_uc011dah.1_Silent_p.V310V	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	446	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGACAACGTCCCCGCCTTCA	0.577													43	68	---	---	---	---	PASS
PPP2R2B	5521	broad.mit.edu	37	5	146257812	146257812	+	5'UTR	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146257812G>A	uc003loe.2	-	1					PPP2R2B_uc010jgm.2_5'UTR|PPP2R2B_uc003log.3_Intron|PPP2R2B_uc003lof.3_Intron|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_004576	NP_004567	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CGGCAATGGAGCTGTCACCTC	0.657													4	5	---	---	---	---	PASS
GMDS	2762	broad.mit.edu	37	6	1961046	1961046	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1961046T>A	uc003mtq.2	-	5	690	c.500A>T	c.(499-501)CAG>CTG	p.Q167L		NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase	167					'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		GGTCTCCTTCTGGGGTATTTC	0.512													5	241	---	---	---	---	PASS
RIPK1	8737	broad.mit.edu	37	6	3081329	3081329	+	Silent	SNP	T	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3081329T>C	uc010jni.2	+	4	670	c.438T>C	c.(436-438)GTT>GTC	p.V146V	RIPK1_uc003muv.3_5'UTR|RIPK1_uc003muw.3_Silent_p.V81V|RIPK1_uc011dhs.1_Intron|RIPK1_uc003mux.2_Silent_p.V146V	NM_003804	NP_003795	Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine	146	Protein kinase.				activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				ATATCCTTGTTGATAATGACT	0.368													72	164	---	---	---	---	PASS
ERVFRDE1	405754	broad.mit.edu	37	6	11104942	11104942	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11104942C>T	uc003mzt.2	-	2	972	c.602G>A	c.(601-603)AGT>AAT	p.S201N	LOC221710_uc003mzr.2_Intron|LOC221710_uc011dio.1_Intron	NM_207582	NP_997465	P60508	EFRD1_HUMAN	syncytin 2	201	Extracellular (Potential).					integral to membrane|plasma membrane|virion					0						GTTTCGAGTACTGCATGAGCT	0.453													20	38	---	---	---	---	PASS
PGBD1	84547	broad.mit.edu	37	6	28269985	28269985	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28269985C>T	uc003nky.2	+	7	2724	c.2354C>T	c.(2353-2355)GCT>GTT	p.A785V	PGBD1_uc003nkz.2_Missense_Mutation_p.A785V	NM_032507	NP_115896	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	785					viral reproduction	membrane|nucleus	scavenger receptor activity|sequence-specific DNA binding transcription factor activity			ovary(4)	4						AACCCAGGTGCTTCTCTAGAC	0.418													21	45	---	---	---	---	PASS
FGD2	221472	broad.mit.edu	37	6	36981690	36981690	+	Intron	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36981690C>G	uc010jwp.1	+						FGD2_uc003ong.2_5'UTR|FGD2_uc011dtv.1_Intron|FGD2_uc003oni.1_Intron	NM_173558	NP_775829	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|early endosome membrane|Golgi apparatus|lamellipodium|nucleus|ruffle membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			upper_aerodigestive_tract(1)|lung(1)|pancreas(1)	3						GCCTGACCCACCTCCCTTCTC	0.642													11	26	---	---	---	---	PASS
SLC22A7	10864	broad.mit.edu	37	6	43267765	43267765	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43267765C>T	uc003out.2	+	5	887	c.788C>T	c.(787-789)GCT>GTT	p.A263V	SLC22A7_uc010jyl.1_Missense_Mutation_p.A264V|SLC22A7_uc003ous.2_Missense_Mutation_p.A261V	NM_153320	NP_696961	Q9Y694	S22A7_HUMAN	solute carrier family 22 member 7 isoform b	263	Helical; (Potential).					basolateral plasma membrane|integral to plasma membrane|membrane fraction	anion:anion antiporter activity|sodium-independent organic anion transmembrane transporter activity				0			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			CTTCTGCTAGCTGTCACCCTG	0.597													61	115	---	---	---	---	PASS
TFAP2D	83741	broad.mit.edu	37	6	50740396	50740396	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50740396C>T	uc003paf.2	+	8	1690	c.1178C>T	c.(1177-1179)GCA>GTA	p.A393V	TFAP2D_uc011dwt.1_RNA	NM_172238	NP_758438	Q7Z6R9	AP2D_HUMAN	transcription factor AP-2 beta-like 1	393	H-S-H (helix-span-helix), dimerization.						DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)					GCAATATGTGCAGCTCTAAGC	0.443													4	92	---	---	---	---	PASS
LRRC1	55227	broad.mit.edu	37	6	53787556	53787556	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53787556A>C	uc003pcd.1	+	14	1817	c.1540A>C	c.(1540-1542)AAT>CAT	p.N514H		NM_018214	NP_060684	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	514						cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		AAACGAGGTCAATCATGCCAT	0.468													71	125	---	---	---	---	PASS
WTAP	9589	broad.mit.edu	37	6	160176079	160176079	+	Silent	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160176079C>A	uc003qsl.2	+	8	849	c.627C>A	c.(625-627)ATC>ATA	p.I209I	WTAP_uc003qso.2_Silent_p.I90I	NM_004906	NP_004897	Q15007	FL2D_HUMAN	Wilms' tumour 1-associating protein isoform 1	209					cell cycle|mRNA processing|RNA splicing	nuclear membrane|nucleolus					0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		ACTTCATCATCCAGCTTGATG	0.448													44	36	---	---	---	---	PASS
TRA2A	29896	broad.mit.edu	37	7	23547080	23547080	+	Silent	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23547080C>T	uc003swi.2	-	5	814	c.600G>A	c.(598-600)GCG>GCA	p.A200A	TRA2A_uc011jzb.1_RNA|TRA2A_uc011jzc.1_Silent_p.A99A|TRA2A_uc011jzd.1_Silent_p.A99A	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha	200	Linker.				nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						TTGGTGTGTGCGCTCTCTTGG	0.418													250	494	---	---	---	---	PASS
NPC1L1	29881	broad.mit.edu	37	7	44561397	44561397	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44561397T>G	uc003tlb.2	-	12	2923	c.2867A>C	c.(2866-2868)GAC>GCC	p.D956A	NPC1L1_uc003tlc.2_Missense_Mutation_p.D956A|NPC1L1_uc011kbw.1_Missense_Mutation_p.D910A|NPC1L1_uc003tla.2_5'Flank	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	956	Cytoplasmic (Potential).				cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5					Ezetimibe(DB00973)	GTCAATGAAGTCATCCACCCA	0.607													35	68	---	---	---	---	PASS
GAL3ST4	79690	broad.mit.edu	37	7	99764823	99764823	+	5'UTR	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99764823G>A	uc003utt.2	-	1					GAL3ST4_uc003utu.2_5'UTR|GAL3ST4_uc010lgq.2_Missense_Mutation_p.S5F	NM_024637	NP_078913	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4						cell-cell signaling|oligosaccharide metabolic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi cisterna membrane|integral to membrane|membrane fraction	3'-phosphoadenosine 5'-phosphosulfate binding|galactosylceramide sulfotransferase activity|proteoglycan sulfotransferase activity			ovary(3)	3	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACTGGTTGGAGATCGGGGGGT	0.592													4	16	---	---	---	---	PASS
SPDYE6	729597	broad.mit.edu	37	7	101987609	101987609	+	3'UTR	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101987609G>A	uc011kkp.1	-	8					SPDYE6_uc003uzb.2_3'UTR	NM_001146210	NP_001139682	P0CI01	SPDE6_HUMAN	speedy homolog E6												0						TCTGCCATTAGCATTGGAATA	0.488													4	41	---	---	---	---	PASS
AKR1B1	231	broad.mit.edu	37	7	134132285	134132285	+	Intron	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134132285C>T	uc003vrp.1	-						AKR1B1_uc003vrq.1_RNA	NM_001628	NP_001619	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1						C21-steroid hormone biosynthetic process|carbohydrate metabolic process|response to stress	cytosol|extracellular space|nucleus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding			ovary(3)	3					NADH(DB00157)|Sulindac(DB00605)	cagctagcaacaggtaggcga	0.070													8	12	---	---	---	---	PASS
TRIM24	8805	broad.mit.edu	37	7	138189041	138189041	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138189041T>C	uc003vuc.2	+	2	586	c.371T>C	c.(370-372)GTC>GCC	p.V124A	TRIM24_uc003vub.2_Missense_Mutation_p.V124A	NM_015905	NP_056989	O15164	TIF1A_HUMAN	transcriptional intermediary factor 1 alpha	124					cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8						CCAGTTGGAGTCATTCGTTGC	0.358													7	194	---	---	---	---	PASS
KIAA1147	57189	broad.mit.edu	37	7	141357344	141357344	+	3'UTR	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141357344C>G	uc003vwk.2	-	9						NM_001080392	NP_001073861	A4D1U4	LCHN_HUMAN	hypothetical protein LOC57189											ovary(1)	1	Melanoma(164;0.0171)					TTTAAAACATCCTGCCTCATC	0.378													4	11	---	---	---	---	PASS
ZNF212	7988	broad.mit.edu	37	7	148952668	148952668	+	3'UTR	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148952668A>G	uc003wfp.2	+	5						NM_012256	NP_036388	Q9UDV6	ZN212_HUMAN	zinc finger protein 212						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			CTTAGAATAAAACTTGCTACT	0.483													56	92	---	---	---	---	PASS
TEX15	56154	broad.mit.edu	37	8	30702516	30702516	+	Missense_Mutation	SNP	C	T	T	rs148542296		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30702516C>T	uc003xil.2	-	1	4018	c.4018G>A	c.(4018-4020)GCT>ACT	p.A1340T		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1340										ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GTCACTGCAGCGGCTGATAAC	0.388													83	166	---	---	---	---	PASS
XKR4	114786	broad.mit.edu	37	8	56015738	56015738	+	Silent	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56015738C>T	uc003xsf.2	+	1	722	c.690C>T	c.(688-690)GGC>GGT	p.G230G		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	230						integral to membrane		p.G230G(1)		pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			CCAACAGCGGCAGCAACAGCA	0.647													3	18	---	---	---	---	PASS
KLF9	687	broad.mit.edu	37	9	73028059	73028059	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73028059C>A	uc004aht.2	-	1	1515	c.221G>T	c.(220-222)CGA>CTA	p.R74L		NM_001206	NP_001197	Q13886	KLF9_HUMAN	Kruppel-like factor 9	74					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CTGGATGGGTCGGTACTTGTT	0.592													16	30	---	---	---	---	PASS
COL15A1	1306	broad.mit.edu	37	9	101817583	101817583	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101817583G>A	uc004azb.1	+	34	3327	c.3121G>A	c.(3121-3123)GAA>AAA	p.E1041K		NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	1041	Triple-helical region 7 (COL7).				angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)				TGAAAAAGGAGAAAAAGGAGA	0.502													51	103	---	---	---	---	PASS
NUP214	8021	broad.mit.edu	37	9	134072982	134072982	+	Silent	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134072982C>G	uc004cag.2	+	29	4212	c.4101C>G	c.(4099-4101)GGC>GGG	p.G1367G	NUP214_uc004cah.2_Silent_p.G1357G|NUP214_uc004cai.2_Silent_p.G797G|NUP214_uc010mzg.2_RNA|NUP214_uc011mcg.1_Silent_p.G193G|NUP214_uc011mcf.1_Silent_p.G144G|NUP214_uc010mzh.1_5'UTR|NUP214_uc010mzi.1_5'UTR	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	1367	Pro/Ser/Thr-rich.|11 X 5 AA approximate repeats.				carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		AGACGTCAGGCGTGCCCTCAG	0.542			T	DEK|SET|ABL1	AML|T-ALL								62	103	---	---	---	---	PASS
CAMSAP1	157922	broad.mit.edu	37	9	138713412	138713412	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138713412C>T	uc004cgr.3	-	11	3095	c.3095G>A	c.(3094-3096)AGT>AAT	p.S1032N	CAMSAP1_uc004cgq.3_Missense_Mutation_p.S922N|CAMSAP1_uc010nbg.2_Missense_Mutation_p.S754N	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	1032						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CTGCAGCGTACTGATGGTTTC	0.522													12	38	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	17151672	17151672	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17151672A>G	uc001ioo.2	-	10	1130	c.1078T>C	c.(1078-1080)TGC>CGC	p.C360R		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	360	EGF-like 5.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TCTGGGTGGCAGCCTCCATTA	0.463													73	135	---	---	---	---	PASS
ZNF37A	7587	broad.mit.edu	37	10	38407244	38407244	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38407244G>T	uc001izk.2	+	8	1984	c.1165G>T	c.(1165-1167)GGG>TGG	p.G389W	ZNF37A_uc001izl.2_Missense_Mutation_p.G389W|ZNF37A_uc001izm.2_Missense_Mutation_p.G389W	NM_001007094	NP_001007095	P17032	ZN37A_HUMAN	zinc finger protein 37a	389	C2H2-type 7.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)	1						CTATGCATGTGGGAAAGCCTT	0.393													4	115	---	---	---	---	PASS
COL13A1	1305	broad.mit.edu	37	10	71692318	71692318	+	Silent	SNP	A	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71692318A>T	uc001jpr.1	+	29	2189	c.1653A>T	c.(1651-1653)GGA>GGT	p.G551G	COL13A1_uc001jqj.1_Intron|COL13A1_uc001jps.1_Silent_p.G522G|COL13A1_uc001jpt.1_Silent_p.G510G|COL13A1_uc001jpu.1_Silent_p.G532G|COL13A1_uc001jpv.1_Silent_p.G551G|COL13A1_uc001jpx.1_Intron|COL13A1_uc001jpw.1_Silent_p.G498G|COL13A1_uc001jpy.1_Silent_p.G489G|COL13A1_uc001jpz.1_Silent_p.G494G|COL13A1_uc001jqa.1_Silent_p.G491G|COL13A1_uc001jqc.1_Intron|COL13A1_uc001jqb.1_Intron|COL13A1_uc001jql.2_Silent_p.G551G|COL13A1_uc001jqd.1_Silent_p.G539G|COL13A1_uc001jqe.1_Silent_p.G534G|COL13A1_uc001jqf.1_Silent_p.G532G|COL13A1_uc001jqg.1_Silent_p.G529G|COL13A1_uc001jqh.1_Silent_p.G551G|COL13A1_uc001jqi.1_Silent_p.G551G|COL13A1_uc010qjf.1_Intron	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1	551	Extracellular (Potential).|Triple-helical region 3 (COL3).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)	GCCCACAGGGAGAGAAAGGAG	0.527													80	213	---	---	---	---	PASS
COL13A1	1305	broad.mit.edu	37	10	71692319	71692319	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71692319G>T	uc001jpr.1	+	29	2190	c.1654G>T	c.(1654-1656)GAG>TAG	p.E552*	COL13A1_uc001jqj.1_Intron|COL13A1_uc001jps.1_Nonsense_Mutation_p.E523*|COL13A1_uc001jpt.1_Nonsense_Mutation_p.E511*|COL13A1_uc001jpu.1_Nonsense_Mutation_p.E533*|COL13A1_uc001jpv.1_Nonsense_Mutation_p.E552*|COL13A1_uc001jpx.1_Intron|COL13A1_uc001jpw.1_Nonsense_Mutation_p.E499*|COL13A1_uc001jpy.1_Nonsense_Mutation_p.E490*|COL13A1_uc001jpz.1_Nonsense_Mutation_p.E495*|COL13A1_uc001jqa.1_Nonsense_Mutation_p.E492*|COL13A1_uc001jqc.1_Intron|COL13A1_uc001jqb.1_Intron|COL13A1_uc001jql.2_Nonsense_Mutation_p.E552*|COL13A1_uc001jqd.1_Nonsense_Mutation_p.E540*|COL13A1_uc001jqe.1_Nonsense_Mutation_p.E535*|COL13A1_uc001jqf.1_Nonsense_Mutation_p.E533*|COL13A1_uc001jqg.1_Nonsense_Mutation_p.E530*|COL13A1_uc001jqh.1_Nonsense_Mutation_p.E552*|COL13A1_uc001jqi.1_Nonsense_Mutation_p.E552*|COL13A1_uc010qjf.1_Intron	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1	552	Extracellular (Potential).|Triple-helical region 3 (COL3).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)	CCCACAGGGAGAGAAAGGAGA	0.532													81	212	---	---	---	---	PASS
STAMBPL1	57559	broad.mit.edu	37	10	90668576	90668576	+	Intron	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90668576A>G	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_Intron|STAMBPL1_uc001kfl.2_Intron|STAMBPL1_uc001kfm.2_RNA	NM_020799	NP_065850	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		CAAATGCTCCATAAGTATCCA	0.403													85	186	---	---	---	---	PASS
PHF21A	51317	broad.mit.edu	37	11	45955418	45955418	+	3'UTR	SNP	A	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45955418A>T	uc001ncc.3	-	18					PHF21A_uc001ncb.3_3'UTR|PHF21A_uc009ykx.2_3'UTR|PHF21A_uc001nca.1_3'UTR	NM_001101802	NP_001095272	Q96BD5	PF21A_HUMAN	BRAF35/HDAC2 complex isoform a						blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2						GAACCAAAAGAATTCTGCACT	0.483													20	24	---	---	---	---	PASS
CD6	923	broad.mit.edu	37	11	60785278	60785278	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60785278C>A	uc001nqq.2	+	11	1853	c.1630C>A	c.(1630-1632)CAC>AAC	p.H544N	CD6_uc001nqp.2_Missense_Mutation_p.H544N|CD6_uc001nqr.2_Missense_Mutation_p.H512N|CD6_uc001nqs.2_RNA|CD6_uc001nqt.2_Missense_Mutation_p.H503N	NM_006725	NP_006716	P30203	CD6_HUMAN	CD6 molecule precursor	544	Cytoplasmic (Potential).				cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1						CAACCCTGGACACTGCATTAC	0.507													27	52	---	---	---	---	PASS
BSCL2	26580	broad.mit.edu	37	11	62473058	62473058	+	5'UTR	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62473058C>G	uc001nuo.1	-	2					BSCL2_uc009yoc.1_5'UTR|BSCL2_uc001nup.2_5'UTR|BSCL2_uc001nuq.1_5'UTR|BSCL2_uc001nur.3_Missense_Mutation_p.G40A|BSCL2_uc009yod.2_Missense_Mutation_p.G40A|BSCL2_uc001nut.3_Missense_Mutation_p.G40A|HNRNPUL2_uc001nuu.1_RNA|GNG3_uc001nuv.2_5'Flank	NM_032667	NP_116056	Q96G97	BSCL2_HUMAN	seipin isoform 2						cell death	integral to endoplasmic reticulum membrane					0						TGGACGCCACCCCTGGCCATG	0.617													4	11	---	---	---	---	PASS
CHRDL2	25884	broad.mit.edu	37	11	74429846	74429846	+	Silent	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74429846C>T	uc001ovi.2	-	2	367	c.114G>A	c.(112-114)AAG>AAA	p.K38K	CHRDL2_uc001ovg.2_5'UTR|CHRDL2_uc001ovh.2_Silent_p.K38K|CHRDL2_uc001ovk.1_Silent_p.K38K			Q6WN34	CRDL2_HUMAN	RecName: Full=Chordin-like protein 2; AltName: Full=Chordin-related protein 2; AltName: Full=Breast tumor novel factor 1;          Short=BNF-1; Flags: Precursor;	38	VWFC 1.				cartilage development|cell differentiation|ossification	extracellular region|mitochondrion					0	Hepatocellular(1;0.098)					GGGAGTATCTCTTCCCATGGA	0.587													3	63	---	---	---	---	PASS
SESN3	143686	broad.mit.edu	37	11	94906296	94906296	+	3'UTR	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94906296C>A	uc001pfk.1	-	10					uc001pfj.2_5'Flank|SESN3_uc010rug.1_3'UTR	NM_144665	NP_653266	P58005	SESN3_HUMAN	sestrin 3						cell cycle arrest	nucleus					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)		AAAAAAAAAACAAACGGCTAA	0.294													3	9	---	---	---	---	PASS
GALNT8	26290	broad.mit.edu	37	12	4874711	4874711	+	Missense_Mutation	SNP	C	T	T	rs147793802	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4874711C>T	uc001qne.1	+	10	1852	c.1760C>T	c.(1759-1761)CCG>CTG	p.P587L		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	587	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(1)|skin(1)	4						GATTTTAAACCGGTGAGTTAT	0.308													7	418	---	---	---	---	PASS
DDX11	1663	broad.mit.edu	37	12	31256928	31256928	+	Silent	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31256928C>G	uc001rjt.1	+	27	3125	c.2874C>G	c.(2872-2874)GGC>GGG	p.G958G	DDX11_uc001rjr.1_3'UTR|DDX11_uc001rjs.1_3'UTR|DDX11_uc001rju.1_3'UTR|DDX11_uc001rjv.1_Silent_p.G958G|DDX11_uc001rjw.1_3'UTR|DDX11_uc009zjn.1_RNA|DDX11_uc009zjo.1_Silent_p.G127G	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	958					G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CAGGCACAGGCGTTAGCTCCC	0.582										Multiple Myeloma(12;0.14)			12	40	---	---	---	---	PASS
KRT86	3892	broad.mit.edu	37	12	52649829	52649829	+	Intron	SNP	T	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52649829T>C	uc010snq.1	+						uc010snr.1_Missense_Mutation_p.K23R	NM_002284	NP_002275	O43790	KRT86_HUMAN	keratin 86						cytoskeleton organization	keratin filament	structural molecule activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.189)		TTACTTCTTCTTGTAACCCTC	0.398													5	78	---	---	---	---	PASS
KRT85	3891	broad.mit.edu	37	12	52760791	52760791	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52760791C>G	uc001sag.2	-	1	519	c.399G>C	c.(397-399)AGG>AGC	p.R133S		NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85	133	Rod.|Coil 1A.				epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		AGGCCGCGAACCTGCTGTTGA	0.617													51	118	---	---	---	---	PASS
CMKLR1	1240	broad.mit.edu	37	12	108686307	108686307	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108686307C>T	uc009zuw.2	-	3	624	c.433G>A	c.(433-435)GTC>ATC	p.V145I	CMKLR1_uc001tmw.2_Missense_Mutation_p.V145I|CMKLR1_uc001tmv.2_Missense_Mutation_p.V143I|CMKLR1_uc009zuv.2_Missense_Mutation_p.V145I	NM_001142345	NP_001135817	Q99788	CML1_HUMAN	chemokine-like receptor 1 isoform a	145	Cytoplasmic (Potential).				chemotaxis|immune response|negative regulation of interleukin-12 production|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage chemotaxis|regulation of calcium-mediated signaling|skeletal system development	integral to plasma membrane	chemokine receptor activity			lung(3)|ovary(1)|pancreas(1)	5						TGGGACCAGACAGGGAGGAGC	0.557													37	60	---	---	---	---	PASS
ACADS	35	broad.mit.edu	37	12	121176678	121176678	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121176678G>A	uc001tza.3	+	8	1107	c.989G>A	c.(988-990)CGC>CAC	p.R330H	ACADS_uc010szl.1_Missense_Mutation_p.R326H|ACADS_uc001tzb.3_Missense_Mutation_p.R211H	NM_000017	NP_000008	P16219	ACADS_HUMAN	short-chain acyl-CoA dehydrogenase precursor	330						mitochondrial matrix	butyryl-CoA dehydrogenase activity			central_nervous_system(2)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)	Lung NSC(355;0.163)			NADH(DB00157)	CTGACCTGGCGCGCTGCCATG	0.642													6	16	---	---	---	---	PASS
DCLK1	9201	broad.mit.edu	37	13	36521538	36521538	+	Silent	SNP	C	T	T	rs146364649	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36521538C>T	uc001uvf.2	-	4	1013	c.780G>A	c.(778-780)CCG>CCA	p.P260P		NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1	260	Doublecortin 2.				cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		GGAACTTCTCCGGTCCACATG	0.423													155	266	---	---	---	---	PASS
DGKH	160851	broad.mit.edu	37	13	42740809	42740809	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42740809G>A	uc001uyl.1	+	9	1138	c.1117G>A	c.(1117-1119)GGT>AGT	p.G373S	DGKH_uc010tfh.1_Missense_Mutation_p.G373S|DGKH_uc001uym.1_Missense_Mutation_p.G373S|DGKH_uc010tfi.1_Missense_Mutation_p.G128S|DGKH_uc010tfj.1_Missense_Mutation_p.G228S|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.G228S|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	373	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TCCTCATTTAGGGTAACTGAT	0.358													111	198	---	---	---	---	PASS
MED4	29079	broad.mit.edu	37	13	48669206	48669206	+	Silent	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48669206C>G	uc001vby.1	-	1	35	c.9G>C	c.(7-9)GCG>GCC	p.A3A	MED4_uc010tge.1_Silent_p.A3A|MED4_uc010tgf.1_5'UTR	NM_014166	NP_054885	Q9NPJ6	MED4_HUMAN	mediator complex subunit 4	3					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		all_cancers(8;2.93e-25)|all_epithelial(8;4.38e-13)|all_lung(13;7.37e-06)|all_hematologic(8;8.61e-05)|Breast(56;0.000141)|Lung NSC(96;0.000518)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.00559)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;5.18e-07)		CACTCGAAGACGCAGCCATTT	0.662											OREG0022406	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	11	---	---	---	---	PASS
SIX4	51804	broad.mit.edu	37	14	61190108	61190108	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61190108A>T	uc001xfc.2	-	1	685	c.685T>A	c.(685-687)TGT>AGT	p.C229S	SIX4_uc010app.1_Missense_Mutation_p.C221S	NM_017420	NP_059116	Q9UIU6	SIX4_HUMAN	sine oculis homeobox homolog 4	229	Homeobox.					nucleus				breast(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		TCCTTGAAACAATACACCGTC	0.652													19	44	---	---	---	---	PASS
HIF1A	3091	broad.mit.edu	37	14	62200986	62200986	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62200986T>A	uc001xfq.2	+	8	1415	c.1011T>A	c.(1009-1011)TGT>TGA	p.C337*	HIF1A_uc001xfr.2_Nonsense_Mutation_p.C337*|HIF1A_uc001xfs.2_Nonsense_Mutation_p.C338*	NM_001530	NP_001521	Q16665	HIF1A_HUMAN	hypoxia-inducible factor 1, alpha subunit	337	Interaction with TSGA10 (By similarity).|PAC.				cellular response to hypoxia|collagen metabolic process|connective tissue replacement involved in inflammatory response wound healing|elastin metabolic process|epithelial to mesenchymal transition|oxygen homeostasis|positive regulation of chemokine production|positive regulation of epithelial cell migration|positive regulation of hormone biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|regulation of transforming growth factor-beta2 production	cytoplasm|nucleolus|transcription factor complex	histone acetyltransferase binding|Hsp90 protein binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			kidney(3)|lung(1)	4				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)		GCATTGTATGTGTGAATTACG	0.353													65	162	---	---	---	---	PASS
DCAF5	8816	broad.mit.edu	37	14	69520975	69520975	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69520975C>T	uc001xkp.2	-	9	2647	c.2428G>A	c.(2428-2430)GGC>AGC	p.G810S	DCAF5_uc001xkq.2_Missense_Mutation_p.G809S	NM_003861	NP_003852	Q96JK2	DCAF5_HUMAN	WD repeat domain 22	810						CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)	2						GGACAGTTGCCAGACCCGCTG	0.587													72	112	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102510612	102510612	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102510612G>A	uc001yks.2	+	71	12850	c.12686G>A	c.(12685-12687)GGC>GAC	p.G4229D		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	4229					cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						CTCCCCCAGGGCAGGCAGAAC	0.602													8	14	---	---	---	---	PASS
TDRD9	122402	broad.mit.edu	37	14	104441754	104441754	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104441754G>C	uc001yom.3	+	7	905	c.875G>C	c.(874-876)TGT>TCT	p.C292S	TDRD9_uc001yon.3_Missense_Mutation_p.C30S	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	292	Helicase ATP-binding.				cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				ACCATCAGCTGTAAAGAGTTT	0.373													198	398	---	---	---	---	PASS
LPCAT4	254531	broad.mit.edu	37	15	34651395	34651395	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34651395G>A	uc001zig.2	-	14	1602	c.1508C>T	c.(1507-1509)TCA>TTA	p.S503L		NM_153613	NP_705841	Q643R3	LPCT4_HUMAN	lysophosphatidylcholine acyltransferase 4	503					phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity|calcium ion binding				0						GCCTGGGGATGAGGCATTTGG	0.607													110	209	---	---	---	---	PASS
VPS18	57617	broad.mit.edu	37	15	41188258	41188258	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41188258G>C	uc001zne.2	+	2	553	c.214G>C	c.(214-216)GGC>CGC	p.G72R		NM_020857	NP_065908	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18	72					endosome organization|lysosome organization|protein transport	HOPS complex|late endosome membrane|lysosomal membrane	metal ion binding|protein binding			ovary(2)|large_intestine(1)	3		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CATGAGCCTGGGCAAGGATAC	0.517													31	71	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44859650	44859650	+	Silent	SNP	T	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44859650T>C	uc001ztx.2	-	36	6757	c.6726A>G	c.(6724-6726)CAA>CAG	p.Q2242Q	SPG11_uc010bdw.2_Silent_p.Q372Q|SPG11_uc010ueh.1_Silent_p.Q2129Q|SPG11_uc010uei.1_Silent_p.Q2242Q	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	2242	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TCAATTTCAGTTGGATGCGGG	0.498													4	75	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54614257	54614257	+	Silent	SNP	T	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54614257T>G	uc002ack.2	+	12	4389	c.4389T>G	c.(4387-4389)GTT>GTG	p.V1463V	UNC13C_uc002acl.2_Silent_p.V293V	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1463					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ACATACAGGTTTCTGCCTCAG	0.393													9	370	---	---	---	---	PASS
LOC645752	645752	broad.mit.edu	37	15	78207580	78207580	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78207580G>T	uc010bky.2	-	18	2096	c.1332C>A	c.(1330-1332)GAC>GAA	p.D444E	LOC645752_uc010umq.1_Missense_Mutation_p.D91E|uc002bcw.1_5'Flank|uc002bcx.1_5'Flank	NR_027024				SubName: Full=GOLGA6 protein; Flags: Fragment;												0						CAGTGGGGTTGTCATGGGGAG	0.577													38	21	---	---	---	---	PASS
HBA2	3040	broad.mit.edu	37	16	223707	223707	+	3'UTR	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:223707G>C	uc002cfv.3	+	3					HBA2_uc002cfw.2_Intron|HBA1_uc002cfx.1_5'Flank|HBA1_uc002cfy.1_5'Flank	NM_000517	NP_000508	P69905	HBA_HUMAN	alpha 2 globin						hydrogen peroxide catabolic process|positive regulation of cell death|protein heterooligomerization	cytosolic small ribosomal subunit|haptoglobin-hemoglobin complex|hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity|protein binding				0		all_cancers(16;2.03e-06)|all_epithelial(16;5.16e-06)|Hepatocellular(16;0.000325)|Lung NSC(18;0.0138)|all_lung(18;0.0306)			Amodiaquine(DB00613)|Chloroquine(DB00608)|Iron Dextran(DB00893)|Mefloquine(DB00358)|Primaquine(DB01087)|Quinine(DB00468)	TGAGTGGGCAGCAGCCTGTGT	0.607											OREG0003686	type=REGULATORY REGION|Gene=SERPINB9|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	17	---	---	---	---	PASS
PRKCB	5579	broad.mit.edu	37	16	24185869	24185869	+	Silent	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24185869G>C	uc002dmd.2	+	12	1559	c.1362G>C	c.(1360-1362)CTG>CTC	p.L454L	PRKCB_uc002dme.2_Silent_p.L454L	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1	454	Protein kinase.				apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	CCATCGGTCTGTTCTTCTTAC	0.428													26	274	---	---	---	---	PASS
ITGAM	3684	broad.mit.edu	37	16	31283265	31283265	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31283265C>T	uc002ebq.2	+	7	754	c.656C>T	c.(655-657)ACG>ATG	p.T219M	ITGAM_uc002ebr.2_Missense_Mutation_p.T219M	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor	219	VWFA.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						AAGCCAATAACGCAGCTGCTT	0.502													4	93	---	---	---	---	PASS
KCTD19	146212	broad.mit.edu	37	16	67324887	67324887	+	Silent	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67324887G>C	uc002esu.2	-	15	2619	c.2568C>G	c.(2566-2568)ACC>ACG	p.T856T	KCTD19_uc002est.2_Silent_p.T628T|KCTD19_uc010vjj.1_Silent_p.T599T	NM_001100915	NP_001094385	Q17RG1	KCD19_HUMAN	potassium channel tetramerisation domain	856						voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		TGATGTGCAGGGTCTGCCAGG	0.617													10	47	---	---	---	---	PASS
CCDC42	146849	broad.mit.edu	37	17	8647475	8647475	+	Silent	SNP	C	T	T	rs149123321		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8647475C>T	uc002gln.2	-	2	338	c.111G>A	c.(109-111)TCG>TCA	p.S37S	CCDC42_uc002glo.2_Silent_p.S37S	NM_144681	NP_653282	Q96M95	CCD42_HUMAN	coiled-coil domain containing 42 isoform 1	37										ovary(1)	1						ATGGGGACTCCGACGCCCCCT	0.547													73	275	---	---	---	---	PASS
GGNBP2	79893	broad.mit.edu	37	17	34943427	34943427	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34943427A>C	uc002hnb.2	+	13	1891	c.1642A>C	c.(1642-1644)ATC>CTC	p.I548L		NM_024835	NP_079111	Q9H3C7	GGNB2_HUMAN	zinc finger protein 403	548					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GTGGTATCAGATCCAGAAGCT	0.318													39	55	---	---	---	---	PASS
PLEKHM1	9842	broad.mit.edu	37	17	43552739	43552739	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43552739T>C	uc002ija.2	-	4	820	c.650A>G	c.(649-651)AAG>AGG	p.K217R	PLEKHM1_uc010wjm.1_Missense_Mutation_p.K189R|PLEKHM1_uc002ijb.2_5'UTR|PLEKHM1_uc010wjn.1_Missense_Mutation_p.K166R|hsa-mir-4315-1|MI0015844_RNA	NM_014798	NP_055613	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M	217					intracellular signal transduction	cytoplasm	metal ion binding				0	Renal(3;0.0405)					CAGAGATTCCTTCCGCTGTAG	0.532													37	60	---	---	---	---	PASS
ABCA8	10351	broad.mit.edu	37	17	66924117	66924117	+	Silent	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66924117A>G	uc002jhp.2	-	9	1392	c.1213T>C	c.(1213-1215)TTG>CTG	p.L405L	ABCA8_uc002jhq.2_Silent_p.L405L|ABCA8_uc010wqq.1_Silent_p.L405L|ABCA8_uc010wqr.1_Silent_p.L344L|ABCA8_uc002jhr.2_Silent_p.L405L	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	405	Helical; (Potential).					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					TCAAATGCCAACATGAAATTT	0.318													84	145	---	---	---	---	PASS
L3MBTL4	91133	broad.mit.edu	37	18	6215828	6215828	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6215828G>C	uc002kmz.3	-	11	951	c.791C>G	c.(790-792)CCC>CGC	p.P264R	L3MBTL4_uc010dkt.2_Missense_Mutation_p.P264R|L3MBTL4_uc002kmy.3_Missense_Mutation_p.P102R	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4	264					chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				TTCTGGATTGGGATAACCTGA	0.323													27	60	---	---	---	---	PASS
ROCK1	6093	broad.mit.edu	37	18	18571174	18571174	+	Silent	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18571174A>G	uc002kte.2	-	18	3047	c.2106T>C	c.(2104-2106)CAT>CAC	p.H702H		NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein	702	Glu-rich.|Interaction with FHOD1.				actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)					CAATAGATTGATGTTTGTCAG	0.303													28	717	---	---	---	---	PASS
ZNF521	25925	broad.mit.edu	37	18	22806642	22806642	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22806642A>C	uc002kvk.2	-	4	1487	c.1240T>G	c.(1240-1242)TTA>GTA	p.L414V	ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Missense_Mutation_p.L414V|ZNF521_uc002kvl.2_Missense_Mutation_p.L194V	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	414	C2H2-type 9; degenerate.				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)					CTTGAAAATAATTGTTTGTTG	0.453			T	PAX5	ALL								44	79	---	---	---	---	PASS
HDHD2	84064	broad.mit.edu	37	18	44660868	44660868	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44660868T>A	uc002lcs.2	-	3	442	c.309A>T	c.(307-309)AAA>AAT	p.K103N	HDHD2_uc002lct.2_Missense_Mutation_p.K13N	NM_032124	NP_115500	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain	103							hydrolase activity				0						TTCCCCTACCTTTGAAATCAG	0.363													5	243	---	---	---	---	PASS
ZNF532	55205	broad.mit.edu	37	18	56601783	56601783	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56601783C>T	uc002lho.2	+	5	3012	c.2465C>T	c.(2464-2466)TCG>TTG	p.S822L	ZNF532_uc002lhp.2_Missense_Mutation_p.S820L|ZNF532_uc010xeg.1_Missense_Mutation_p.S820L|ZNF532_uc002lhr.2_Missense_Mutation_p.S820L|ZNF532_uc002lhs.2_Missense_Mutation_p.S820L	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	822			S -> L (in a breast cancer sample; somatic mutation).		regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	p.S822L(1)		breast(1)|skin(1)	2						ATCTGCAGGTCGGTGCACTTC	0.502													19	207	---	---	---	---	PASS
JSRP1	126306	broad.mit.edu	37	19	2252973	2252973	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2252973C>A	uc002lvi.1	-	5	501	c.466G>T	c.(466-468)GCA>TCA	p.A156S	JSRP1_uc002lvj.1_Missense_Mutation_p.A156S	NM_144616	NP_653217	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	156	Pro-rich.					sarcoplasmic reticulum membrane				pancreas(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCACACGTGCTTGGAGTGCT	0.692													9	19	---	---	---	---	PASS
CELF5	60680	broad.mit.edu	37	19	3293438	3293438	+	Silent	SNP	C	A	A	rs142809979		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3293438C>A	uc002lxm.2	+	12	1489	c.1452C>A	c.(1450-1452)CCC>CCA	p.P484P	CELF5_uc002lxl.1_3'UTR|CELF5_uc010dtj.1_3'UTR|CELF5_uc010xhg.1_3'UTR|CELF5_uc002lxn.2_RNA	NM_021938	NP_068757	Q8N6W0	CELF5_HUMAN	bruno-like 5, RNA binding protein	484					mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding			ovary(2)	2						CGGGACACCCCTACTGACCGC	0.687													21	94	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14743789	14743789	+	Silent	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14743789A>G	uc002mzi.3	-	13	1735	c.1587T>C	c.(1585-1587)ATT>ATC	p.I529I	EMR3_uc010dzp.2_Silent_p.I477I|EMR3_uc010xnv.1_Silent_p.I403I	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	529	Helical; Name=5; (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						TTCTTTTCAAAATCCAAAAGA	0.393													19	326	---	---	---	---	PASS
ZNF675	171392	broad.mit.edu	37	19	23836056	23836056	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23836056C>G	uc002nri.2	-	4	1861	c.1679G>C	c.(1678-1680)GGA>GCA	p.G560A		NM_138330	NP_612203	Q8TD23	ZN675_HUMAN	zinc finger protein 675	560					bone resorption|cytokine-mediated signaling pathway|hemopoiesis|I-kappaB kinase/NF-kappaB cascade|negative regulation of JNK cascade|negative regulation of osteoclast differentiation|negative regulation of protein kinase activity|negative regulation of transcription, DNA-dependent|regulation of ossification|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|kidney(1)	2		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TAGTTTCTCTCCAGTATGTAT	0.303													20	637	---	---	---	---	PASS
HKR1	284459	broad.mit.edu	37	19	37853658	37853658	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37853658A>G	uc002ogb.2	+	6	1230	c.961A>G	c.(961-963)AGG>GGG	p.R321G	HKR1_uc002ofx.2_Missense_Mutation_p.R37G|HKR1_uc002ofy.2_Missense_Mutation_p.R37G|HKR1_uc002oga.2_Missense_Mutation_p.R303G|HKR1_uc010xto.1_Missense_Mutation_p.R303G|HKR1_uc002ogc.2_Missense_Mutation_p.R302G|HKR1_uc010xtp.1_Missense_Mutation_p.R260G|HKR1_uc002ogd.2_Missense_Mutation_p.R260G	NM_181786	NP_861451	P10072	HKR1_HUMAN	GLI-Kruppel family member HKR1	321	C2H2-type 1.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CACACATCAGAGGACACACTC	0.507													15	37	---	---	---	---	PASS
PLA2G4C	8605	broad.mit.edu	37	19	48613788	48613788	+	5'UTR	SNP	T	G	G	rs138501838	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48613788T>G	uc002phx.2	-	1					PLA2G4C_uc010elr.2_5'UTR|PLA2G4C_uc010xzd.1_5'UTR|PLA2G4C_uc002phy.3_5'UTR	NM_003706	NP_003697	Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC isoform 1 precursor						arachidonic acid metabolic process|glycerophospholipid catabolic process|inflammatory response|intracellular signal transduction|parturition	cytosol|membrane	calcium-independent phospholipase A2 activity|phospholipid binding			ovary(1)|skin(1)	2		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		GTGGAGCTTGTGCTCCGGAAT	0.582													5	31	---	---	---	---	PASS
MAMSTR	284358	broad.mit.edu	37	19	49216785	49216785	+	Silent	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49216785C>T	uc002pkg.2	-	10	1049	c.987G>A	c.(985-987)CTG>CTA	p.L329L	MAMSTR_uc002pkf.2_Silent_p.L226L	NM_001130915	NP_001124387	Q6ZN01	MASTR_HUMAN	MEF2 activating motif and SAP domain containing	329	Pro-rich.|Transcription activation (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding			ovary(1)	1						CAGGGAAGTCCAGGGGAATAG	0.517											OREG0025608	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	26	---	---	---	---	PASS
FPR3	2359	broad.mit.edu	37	19	52327023	52327023	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52327023C>T	uc002pxt.1	+	2	206	c.22C>T	c.(22-24)CCT>TCT	p.P8S		NM_002030	NP_002021	P25089	FPR3_HUMAN	formyl peptide receptor-like 2	8	Extracellular (Potential).				cellular component movement|chemotaxis	integral to membrane|plasma membrane	N-formyl peptide receptor activity			lung(4)|breast(1)|skin(1)	6						CTTCTCCATTCCTCTGAATGA	0.473													30	62	---	---	---	---	PASS
ZNF17	7565	broad.mit.edu	37	19	57932387	57932387	+	Silent	SNP	T	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57932387T>C	uc002qoo.1	+	3	1758	c.1527T>C	c.(1525-1527)TGT>TGC	p.C509C	ZNF547_uc002qpm.3_Intron|ZNF17_uc002qop.1_Silent_p.C511C	NM_006959	NP_008890	P17021	ZNF17_HUMAN	zinc finger protein 17	509	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		CCTTTAGATGTCGCTCCACAC	0.408													5	120	---	---	---	---	PASS
ZNF274	10782	broad.mit.edu	37	19	58695360	58695360	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58695360T>A	uc002qrq.1	+	2	487	c.28T>A	c.(28-30)TCC>ACC	p.S10T	ZNF274_uc010yhu.1_RNA|ZNF274_uc010yhv.1_Intron|ZNF274_uc002qrr.1_Missense_Mutation_p.S10T|ZNF274_uc002qrs.1_Intron|ZNF274_uc010eum.1_5'UTR	NM_133502	NP_598009	Q96GC6	ZN274_HUMAN	zinc finger protein 274 isoform c	10					viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		GACGGCCTGGTCCTGTGTGAG	0.572													41	64	---	---	---	---	PASS
TMC2	117532	broad.mit.edu	37	20	2616597	2616597	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2616597G>T	uc002wgf.1	+	18	2347	c.2332G>T	c.(2332-2334)GTT>TTT	p.V778F	TMC2_uc002wgg.1_Missense_Mutation_p.V762F	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	778	Cytoplasmic (Potential).					integral to membrane				ovary(3)	3						CCTGAACTCAGTTTCCAAAAG	0.493													29	187	---	---	---	---	PASS
SIGLEC1	6614	broad.mit.edu	37	20	3679976	3679976	+	Silent	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3679976G>A	uc002wja.2	-	7	1659	c.1659C>T	c.(1657-1659)CAC>CAT	p.H553H	SIGLEC1_uc002wiz.3_Silent_p.H553H	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor	553	Ig-like C2-type 5.|Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	10						CGGGACCCTCGTGAAGCAGGG	0.677													3	19	---	---	---	---	PASS
DSCR6	53820	broad.mit.edu	37	21	38390298	38390298	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38390298G>A	uc002yvv.2	+	4	574	c.364G>A	c.(364-366)GAA>AAA	p.E122K	DSCR6_uc011aec.1_Silent_p.P8P|DSCR6_uc010gnd.2_Silent_p.P8P	NM_018962	NP_061835	P57055	DSCR6_HUMAN	Down syndrome critical region protein 6	122						nucleus				breast(1)	1		Myeloproliferative disorder(46;0.0632)				GTCTGCTTCCGAAGCTGAAGA	0.582													16	55	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47980645	47980645	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47980645G>T	uc002zjo.2	+	33	4163	c.3980G>T	c.(3979-3981)GGC>GTC	p.G1327V	DIP2A_uc011afz.1_Missense_Mutation_p.G1323V|DIP2A_uc002zjs.2_5'Flank	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	1327					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GGCACAGCTGGCCCGGACCCC	0.597													4	30	---	---	---	---	PASS
SLC5A1	6523	broad.mit.edu	37	22	32506242	32506242	+	3'UTR	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32506242C>T	uc003amc.2	+	15					SLC5A1_uc011alz.1_3'UTR	NM_000343	NP_000334	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose						carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding			skin(1)	1						TGGACTCTTACTCACCTTCCT	0.448													113	226	---	---	---	---	PASS
NRK	203447	broad.mit.edu	37	X	105132300	105132300	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105132300A>C	uc004emd.2	+	5	569	c.266A>C	c.(265-267)GAT>GCT	p.D89A	NRK_uc010npc.1_5'UTR	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	89	Protein kinase.						ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14						GAGGAAGAGGATCTCAGGACT	0.423										HNSCC(51;0.14)			123	236	---	---	---	---	PASS
FMR1NB	158521	broad.mit.edu	37	X	147088242	147088242	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147088242C>T	uc004fcm.2	+	3	492	c.418C>T	c.(418-420)CAG>TAG	p.Q140*		NM_152578	NP_689791	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor	140	P-type.|Extracellular (Potential).					integral to membrane				ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					GAGGGAAAATCAGGTGGCAAA	0.378													160	312	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11559	11559	+	RNA	SNP	G	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11559G>C	uc004cov.3	+	1		c.982G>C			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		ACTATCCCTATGAGGCATAAT	0.443													4	19	---	---	---	---	PASS
TNFRSF25	8718	broad.mit.edu	37	1	6524881	6524883	+	Intron	DEL	GGC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6524881_6524883delGGC	uc001ane.2	-						TNFRSF25_uc001ana.2_Intron|TNFRSF25_uc001anb.2_Intron|TNFRSF25_uc001anc.2_Intron|TNFRSF25_uc001and.2_Intron|TNFRSF25_uc009vlz.2_Intron|TNFRSF25_uc001anf.2_Intron|TNFRSF25_uc001ang.2_Intron|TNFRSF25_uc001anh.2_Intron|TNFRSF25_uc001ani.1_Intron	NM_003790	NP_003781	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily,						apoptosis|induction of apoptosis by extracellular signals	cytosol|extracellular region|integral to plasma membrane	tumor necrosis factor receptor activity			central_nervous_system(2)|breast(1)	3	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		GACAGAAATAGGCGAAAGACAGA	0.537													4	4	---	---	---	---	
EXOSC10	5394	broad.mit.edu	37	1	11131667	11131668	+	Intron	INS	-	CT	CT	rs146687816	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11131667_11131668insCT	uc001asa.2	-						EXOSC10_uc001asb.2_Intron	NM_001001998	NP_001001998	Q01780	EXOSX_HUMAN	exosome component 10 isoform 1						CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		cacttccccccgtctgctcagc	0.000													6	6	---	---	---	---	
MTF1	4520	broad.mit.edu	37	1	38300956	38300956	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38300956delC	uc001cce.1	-						MTF1_uc009vvj.1_Intron	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ATCTACCTTTCCCTAATAGAG	0.343													97	62	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39770238	39770238	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39770238delT	uc010ois.1	+						MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc009vvq.1_Intron|MACF1_uc001cdb.1_Intron	NM_012090	NP_036222	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			cttttctttcttttttttttt	0.159													5	3	---	---	---	---	
PPIH	10465	broad.mit.edu	37	1	43131362	43131362	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43131362delA	uc001chq.2	+						PPIH_uc009vwl.2_Intron	NM_006347	NP_006338	O43447	PPIH_HUMAN	peptidylprolyl isomerase H						protein complex assembly|protein folding	cytoplasm|nuclear speck|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity|protein binding|ribonucleoprotein binding				0	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)			L-Proline(DB00172)	cttaaaaaagaaaaaaaaaat	0.000													4	2	---	---	---	---	
KLF17	128209	broad.mit.edu	37	1	44516768	44516768	+	5'UTR	DEL	C	-	-	rs35788737		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44516768delC	uc009vxf.1	+	2						NM_173484	NP_775755	Q5JT82	KLF17_HUMAN	zinc finger protein 393						regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)					aaagaaatggccagttggcaa	0.060													4	4	---	---	---	---	
PIK3R3	8503	broad.mit.edu	37	1	46570597	46570598	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46570597_46570598insA	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)					aagactccatcaaaaaaaaaaa	0.173													11	5	---	---	---	---	
FAM40A	85369	broad.mit.edu	37	1	110589510	110589510	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110589510delA	uc001dza.1	+						FAM40A_uc001dyz.1_Intron|FAM40A_uc009wfp.1_Intron	NM_033088	NP_149079	Q5VSL9	FA40A_HUMAN	hypothetical protein LOC85369							nucleus	protein binding			ovary(3)|large_intestine(1)	4		all_cancers(81;8.51e-05)|all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0154)|all cancers(265;0.0732)|Epithelial(280;0.0781)|Colorectal(144;0.115)|LUSC - Lung squamous cell carcinoma(189;0.137)		cgtctctactaaaaaaaaaaa	0.000													5	3	---	---	---	---	
CASQ2	845	broad.mit.edu	37	1	116311367	116311368	+	5'UTR	DEL	CA	-	-	rs71755438	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116311367_116311368delCA	uc001efx.3	-	1					CASQ2_uc010owu.1_5'UTR	NM_001232	NP_001223	O14958	CASQ2_HUMAN	cardiac calsequestrin 2 precursor						heart development|striated muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		AGAGCAGAGGCAcacacacaca	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143540325	143540325	+	IGR	DEL	G	-	-	rs66944250		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143540325delG								None (None upstream) : LOC100286793 (107314 downstream)																							TGCTGTAGTAGTAACTGCTTC	0.368													7	8	---	---	---	---	
MTMR11	10903	broad.mit.edu	37	1	149903349	149903349	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149903349delA	uc001etl.3	-						MTMR11_uc001etm.1_Intron|MTMR11_uc010pbm.1_Intron|MTMR11_uc010pbn.1_Intron	NM_001145862	NP_001139334	A4FU01	MTMRB_HUMAN	myotubularin related protein 11 isoform a								phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			AGGGACAAAGAAGAGGGGTCC	0.532													44	29	---	---	---	---	
RIT1	6016	broad.mit.edu	37	1	155874708	155874708	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155874708delT	uc001fmh.1	-						RIT1_uc010pgr.1_Intron	NM_006912	NP_008843	Q92963	RIT1_HUMAN	Ras-like without CAAX 1						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			breast(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)			AATGCCCACATTTTCTCAGGA	0.343													53	27	---	---	---	---	
C1orf112	55732	broad.mit.edu	37	1	169791102	169791102	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169791102delA	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc010plu.1_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN	hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CTTAGAAAGTAAAAAAAAAAT	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	202780874	202780878	+	IGR	DEL	CAATT	-	-	rs72442869	byFrequency	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202780874_202780878delCAATT								KDM5B (3325 upstream) : LOC148709 (50004 downstream)																							CTCATCTCTCCAATTCAATGCCATC	0.566													8	8	---	---	---	---	
OPTC	26254	broad.mit.edu	37	1	203473016	203473019	+	Intron	DEL	ACAC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203473016_203473019delACAC	uc001gzu.1	+							NM_014359	NP_055174	Q9UBM4	OPT_HUMAN	opticin precursor							proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.109)			acgcatgcatacacacacacacTC	0.324													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213594066	213594066	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213594066delT								RPS6KC1 (147259 upstream) : PROX1 (567220 downstream)																							TTGACCCCtgtattagcttgt	0.294													4	3	---	---	---	---	
DNAH14	127602	broad.mit.edu	37	1	225307050	225307051	+	Intron	DEL	AT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225307050_225307051delAT	uc001how.2	+							NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						atacttgcacatatatatatac	0.228													4	3	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241501059	241501059	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241501059delT	uc001hyv.2	-						RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			CTCCTCTGACTTCATTTTCAT	0.428													4	2	---	---	---	---	
ZNF670	93474	broad.mit.edu	37	1	247207552	247207552	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247207552delA	uc001icd.1	-						ZNF695_uc001ica.2_Intron|ZNF695_uc001icb.1_Intron	NM_033213	NP_149990	Q9BS34	ZN670_HUMAN	zinc finger protein 670						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00427)			AAATAATTGGAAAAAAAAAAC	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21115713	21115713	+	IGR	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21115713delG								C2orf43 (92886 upstream) : APOB (108589 downstream)																							tcctctctgtgaattgcctat	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23222015	23222015	+	IGR	DEL	A	-	-	rs74518218		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23222015delA								None (None upstream) : KLHL29 (533440 downstream)																							TGAGATTTTGAAAAAAAAAAA	0.373													4	3	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43768645	43768645	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43768645delT	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_Intron|THADA_uc002rta.2_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TCATGCTAAGttttttttttt	0.174													3	6	---	---	---	---	
PREPL	9581	broad.mit.edu	37	2	44549358	44549358	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44549358delG	uc002ruf.2	-						PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Intron|PREPL_uc010fax.2_Intron|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Intron	NM_006036	NP_006027	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like isoform C						proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CTACAGCAATGGATGGGGGTG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56265837	56265837	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56265837delG	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																		TGCTCAACCTGGGCCTTCTAG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	63876903	63876903	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63876903delA								LOC388955 (26744 upstream) : UGP2 (191195 downstream)																							CTTTTCCCAGAAAGGGGGGCT	0.428													4	2	---	---	---	---	
NAT8	9027	broad.mit.edu	37	2	73868466	73868467	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73868466_73868467insT	uc002sji.1	-	2	456_457	c.289_290insA	c.(289-291)ATTfs	p.I97fs		NM_003960	NP_003951	Q9UHE5	NAT8_HUMAN	N-acetyltransferase 8	97	N-acetyltransferase.				gastrulation with mouth forming second|response to drug	integral to membrane	N-acetyltransferase activity			ovary(1)	1						GGATTTGGTAATGTCAGACATG	0.540													97	44	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89100923	89100924	+	Intron	INS	-	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89100923_89100924insG	uc010fhg.2	+						FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_Intron	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						AATATAAAAAAGATACATATGA	0.282													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103741650	103741650	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103741650delT								TMEM182 (307514 upstream) : None (None downstream)																							ACATGTATGATTTTTTTTAAG	0.358													4	2	---	---	---	---	
MERTK	10461	broad.mit.edu	37	2	112779548	112779549	+	Intron	INS	-	A	A	rs112340384		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112779548_112779549insA	uc002thk.1	+						MERTK_uc002thl.1_Intron	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor						cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9						CCGAGATAAGGAAAAAAAAGCA	0.441													3	3	---	---	---	---	
SLC35F5	80255	broad.mit.edu	37	2	114483287	114483287	+	Intron	DEL	G	-	-	rs67850681	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114483287delG	uc002tku.1	-						SLC35F5_uc002tkt.2_Intron	NM_025181	NP_079457	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5						transport	integral to membrane					0						CAACGCCATAGAAAAAAAAAC	0.388													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	128838664	128838665	+	IGR	DEL	TG	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128838664_128838665delTG								SAP130 (53031 upstream) : UGGT1 (10089 downstream)																							ctgttgcacctgtactgtagtt	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129284313	129284313	+	IGR	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129284313delG								HS6ST1 (208142 upstream) : None (None downstream)																							ATCCTTCCCTGGGAGCATGAC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133041342	133041342	+	IGR	DEL	T	-	-	rs62163813		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133041342delT								NCRNA00164 (25800 upstream) : GPR39 (132805 downstream)																							gttgagagcctcaggttgagt	0.109													4	2	---	---	---	---	
R3HDM1	23518	broad.mit.edu	37	2	136380208	136380210	+	Intron	DEL	TGT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136380208_136380210delTGT	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)		TGGGTTTTTGTGTTGTTGTTTTT	0.291													625	272	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142004544	142004544	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142004544delA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		catctcaaagaaaaaaaagaa	0.114										TSP Lung(27;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146094900	146094900	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146094900delA								ZEB2 (816969 upstream) : None (None downstream)																							CCCCAGGGCCAAAAATGCCCA	0.488													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	147123576	147123577	+	IGR	DEL	CA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147123576_147123577delCA								None (None upstream) : PABPC1P2 (221048 downstream)																							GAGTCACCTTCACTCACCCAGC	0.208													4	2	---	---	---	---	
CSRNP3	80034	broad.mit.edu	37	2	166411467	166411467	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166411467delG	uc002udf.2	+							NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3						apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5						cttgctcctcgtctccaacac	0.000													2	4	---	---	---	---	
CSRNP3	80034	broad.mit.edu	37	2	166411469	166411471	+	Intron	DEL	CTC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166411469_166411471delCTC	uc002udf.2	+							NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3						apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5						tgctcctcgtctccaacactctg	0.000													2	4	---	---	---	---	
ITGA6	3655	broad.mit.edu	37	2	173341499	173341500	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173341499_173341500insA	uc002uhp.1	+						ITGA6_uc010zdy.1_Intron|ITGA6_uc002uho.1_Intron|ITGA6_uc010fqm.1_Intron	NM_001079818	NP_001073286	P23229	ITA6_HUMAN	integrin alpha chain, alpha 6 isoform a						blood coagulation|cell adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter	integrin complex	protein binding|receptor activity			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TTTTGATGATGAAAAAAACAAA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206785005	206785007	+	IGR	DEL	AGG	-	-	rs67779539	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206785005_206785007delAGG								NRP2 (122149 upstream) : INO80D (73439 downstream)																							aaagaaagaaaggagaaagaaag	0.172													4	2	---	---	---	---	
GPR1	2825	broad.mit.edu	37	2	207052589	207052589	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207052589delA	uc002vbl.3	-						GPR1_uc010fue.2_Intron|GPR1_uc010fuf.2_Intron	NM_005279	NP_005270	P46091	GPR1_HUMAN	G protein-coupled receptor 1							integral to plasma membrane	G-protein coupled receptor activity				0		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		GGCAGTAACCAAAAATGAAGA	0.294													4	2	---	---	---	---	
TNS1	7145	broad.mit.edu	37	2	218817192	218817193	+	Intron	DEL	CA	-	-	rs35174417		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218817192_218817193delCA	uc010fvk.1	-						TNS1_uc002vgv.1_Intron	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TCTCCCGCGCcacacacacaca	0.421													4	2	---	---	---	---	
RQCD1	9125	broad.mit.edu	37	2	219456821	219456821	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219456821delA	uc010zkh.1	+						RQCD1_uc002vih.1_Intron|RQCD1_uc010zki.1_Intron	NM_005444	NP_005435	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|sex differentiation|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(1)|skin(1)	2		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		aagcctctagaaaaaaaaact	0.104													3	3	---	---	---	---	
MFF	56947	broad.mit.edu	37	2	228207712	228207712	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228207712delA	uc002vos.2	+						MFF_uc002vot.2_Intron|MFF_uc002vou.2_Intron|MFF_uc002vov.2_Intron|MFF_uc002vow.2_Intron|MFF_uc002vox.2_Intron|MFF_uc002voy.2_Intron|MFF_uc002voz.2_Intron	NM_020194	NP_064579	Q9GZY8	MFF_HUMAN	mitochondrial fission factor							integral to membrane|mitochondrial outer membrane				large_intestine(1)	1						TTTATTAAGGAAAAAAAAAAA	0.338													3	4	---	---	---	---	
COL6A3	1293	broad.mit.edu	37	2	238323050	238323051	+	5'Flank	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238323050_238323051insA	uc002vwl.2	-						COL6A3_uc002vwo.2_5'Flank|COL6A3_uc010znj.1_5'Flank|COL6A3_uc002vwq.2_5'Flank|COL6A3_uc002vwr.2_5'Flank|COL6A3_uc010znk.1_5'Flank	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CCCCAACTCTTAAAAAAAAAAA	0.470													4	2	---	---	---	---	
FARP2	9855	broad.mit.edu	37	2	242410258	242410260	+	Intron	DEL	AGG	-	-	rs10534278		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242410258_242410260delAGG	uc002wbi.1	+							NM_014808	NP_055623	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2						axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		TGCTGCTCTCAGGGGACCCTGTT	0.562													9	8	---	---	---	---	
GRM7	2917	broad.mit.edu	37	3	7024299	7024299	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7024299delG	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)	caactcaaaagaaaaaaaaaa	0.020													7	4	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10188296	10188297	+	Frame_Shift_Ins	INS	-	TTTT	TTTT			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188296_10188297insTTTT	uc003bvc.2	+	2	652_653	c.439_440insTTTT	c.(439-441)ATTfs	p.I147fs	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	147	Involved in binding to CCT complex.		I -> T (in pheochromocytoma).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.A149fs*25(4)|p.F148fs*11(3)|p.I147fs*27(2)|p.I147fs*25(1)|p.I147fs*11(1)|p.I147fs*12(1)|p.I147fs*13(1)|p.I147_F148del(1)|p.I147fs*10(1)|p.F148fs*25(1)|p.P146fs*23(1)|p.G144fs*19(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CGGACAGCCTATTTTTGCCAAT	0.416		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				179	96	---	---	---	---	
NEK4	6787	broad.mit.edu	37	3	52752657	52752658	+	Intron	DEL	CC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52752657_52752658delCC	uc003dfq.3	-						NEK4_uc011bej.1_Intron	NM_003157	NP_003148	P51957	NEK4_HUMAN	NIMA-related kinase 4						cell division|mitosis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		ccaatgcctgcccacaaagaaa	0.000													4	2	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65415803	65415805	+	In_Frame_Del	DEL	ACA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65415803_65415805delACA	uc003dmn.2	-	12	2083_2085	c.1557_1559delTGT	c.(1555-1560)ATTGTA>ATA	p.V520del	MAGI1_uc003dmm.2_In_Frame_Del_p.V520del|MAGI1_uc003dmo.2_In_Frame_Del_p.V520del|MAGI1_uc003dmp.2_In_Frame_Del_p.V520del|MAGI1_uc010hny.2_In_Frame_Del_p.V405del	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	520	PDZ 2.				cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		ATTCACACTTACAATCACATCCC	0.448													39	40	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71008187	71008187	+	3'UTR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71008187delT	uc003dol.2	-	17					FOXP1_uc003dom.2_3'UTR|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_3'UTR|FOXP1_uc003dop.2_3'UTR|FOXP1_uc003doq.1_Intron|FOXP1_uc003doi.2_3'UTR|FOXP1_uc003doj.2_3'UTR|FOXP1_uc003dok.2_3'UTR	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		TACAAATTCCTTTTTTCAACA	0.353			T	PAX5	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	82573028	82573028	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82573028delT								GBE1 (762078 upstream) : None (None downstream)																							ACTCAGAACATTTTTTTTTTC	0.413													6	3	---	---	---	---	
CASR	846	broad.mit.edu	37	3	121965611	121965611	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121965611delA	uc003eev.3	+						CASR_uc003eew.3_Intron	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor						anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	gccagactacaagcacaccac	0.229													4	2	---	---	---	---	
LOC729375	729375	broad.mit.edu	37	3	129827935	129827936	+	Intron	INS	-	GGT	GGT			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129827935_129827936insGGT	uc011ble.1	-							NR_024252				Homo sapiens cDNA FLJ42457 fis, clone BRACE2018700.												0						TGTTTTTAAAGAACCTGTGGTT	0.485													6	3	---	---	---	---	
ZIC4	84107	broad.mit.edu	37	3	147113415	147113416	+	Intron	INS	-	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147113415_147113416insC	uc003ewd.1	-						ZIC4_uc003ewc.1_Intron|ZIC4_uc011bno.1_Intron	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN	zinc finger protein of the cerebellum 4							nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2						TTCACCCTTGTCCCCCCCAGAA	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	148831782	148831784	+	IGR	DEL	AAC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148831782_148831784delAAC								HLTF (27441 upstream) : HPS3 (15587 downstream)																							actgaggccaaacagcagcacca	0.000													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	158970337	158970337	+	Intron	DEL	T	-	-	rs79500886		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158970337delT	uc003fcq.1	+						SCHIP1_uc003fcr.1_Intron|IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			CAAAGCCACATTTTTTTTTTC	0.279													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165761992	165761994	+	IGR	DEL	TGT	-	-	rs111477959		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165761992_165761994delTGT								BCHE (206739 upstream) : None (None downstream)																							CTGGGAATAATGTTGTGGGACTG	0.320													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184795567	184795568	+	IGR	INS	-	TGG	TGG			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184795567_184795568insTGG								VPS8 (25165 upstream) : C3orf70 (272 downstream)																							TAAATGCTATTTGGTGGTGGTG	0.470													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197186723	197186723	+	IGR	DEL	G	-	-	rs66563160		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197186723delG								DLG1 (160580 upstream) : BDH1 (49932 downstream)																							gtggtcgggaggggatgCAGT	0.279													4	2	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	66227	66227	+	Intron	DEL	T	-	-	rs28445159		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66227delT	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	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)		taactttttgttttttttttg	0.000													5	3	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54248715	54248715	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54248715delA	uc003haa.2	+						FIP1L1_uc003gzx.3_Intron|FIP1L1_uc011bzt.1_Intron|FIP1L1_uc003gzy.2_Intron|FIP1L1_uc011bzu.1_Intron|FIP1L1_uc003gzz.2_Intron|FIP1L1_uc003hab.2_Intron|FIP1L1_uc003hac.2_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	AGAGGAAAATAGTATGTGCAA	0.358			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			9	4	---	---	---	---	
KDR	3791	broad.mit.edu	37	4	55948902	55948907	+	Intron	DEL	TTCAAA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55948902_55948907delTTCAAA	uc003has.2	-						KDR_uc003hat.1_Intron	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor						angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	AATAGCAACCTTCAAAACATCCTTTA	0.301			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			51	33	---	---	---	---	
FAM13A	10144	broad.mit.edu	37	4	89661365	89661365	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89661365delC	uc003hse.1	-						FAM13A_uc011cdp.1_5'Flank|FAM13A_uc003hsa.1_Intron|FAM13A_uc003hsb.1_Intron|FAM13A_uc003hsd.1_Intron|FAM13A_uc003hsc.1_Intron|FAM13A_uc011cdq.1_Intron|FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsg.1_Intron	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						cttccaacatcccccattctg	0.015													4	2	---	---	---	---	
NHEDC1	150159	broad.mit.edu	37	4	103826510	103826511	+	Intron	DEL	CA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103826510_103826511delCA	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		cctgagtagccaggaCTGGTTA	0.119													9	6	---	---	---	---	
NDST3	9348	broad.mit.edu	37	4	119043395	119043395	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119043395delG	uc003ibx.2	+						NDST3_uc011cgf.1_Intron	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1						GTATGAGGGTGGGGGAGGTCT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152878428	152878429	+	Intron	INS	-	T	T	rs145508638	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152878428_152878429insT	uc003imn.2	+						uc003imo.2_Intron					Homo sapiens cDNA clone IMAGE:5266192.																		ACCAGCCCCCCGGGCTTTGTTC	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179541558	179541559	+	IGR	INS	-	ATC	ATC	rs142664410	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179541558_179541559insATC								LOC285501 (629655 upstream) : None (None downstream)																							GAAAGGCACTTATGACCCAGGA	0.317													2	6	---	---	---	---	
BASP1	10409	broad.mit.edu	37	5	17229016	17229016	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17229016delA	uc003jfx.2	+							NM_006317	NP_006308	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein						glomerular visceral epithelial cell differentiation|negative regulation of transcription, DNA-dependent	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	protein domain specific binding|transcription corepressor activity|transcription regulatory region DNA binding				0						GTAATGCTGCAAAAAATGTTA	0.433													4	2	---	---	---	---	
ZNF366	167465	broad.mit.edu	37	5	71750800	71750800	+	Intron	DEL	C	-	-	rs147614875		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71750800delC	uc003kce.1	-							NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		tgctctgcttccatcatcttt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	78466166	78466168	+	IGR	DEL	TTG	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78466166_78466168delTTG								BHMT (38054 upstream) : JMY (65786 downstream)																							gcTGCAAAATttgttgttgttgt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	83143243	83143243	+	IGR	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83143243delC								HAPLN1 (126347 upstream) : EDIL3 (94883 downstream)																							cacattgatgccctcattttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116791609	116791609	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116791609delG	uc003kry.2	+											Homo sapiens cDNA clone IMAGE:5297581.																		ctggtgatgtggagacacgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119082247	119082248	+	IGR	DEL	TG	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119082247_119082248delTG								FAM170A (110731 upstream) : PRR16 (717771 downstream)																							CGAGGCTTTCtgtgtgtgtgtg	0.312													3	3	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142421513	142421516	+	Intron	DEL	AGTC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142421513_142421516delAGTC	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACTCTGAAAAGTCACCAGGTCTG	0.569													63	32	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156766466	156766468	+	Intron	DEL	TCT	-	-	rs143579103		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156766466_156766468delTCT	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)			aacaattaggtcttctttcattg	0.305													5	3	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168713235	168713238	+	Intron	DEL	AAGC	-	-	rs72277881		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168713235_168713238delAAGC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	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)			ACTATAGAGGAAGCAAAATTATGT	0.343													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172008528	172008528	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172008528delA								SH3PXD2B (127001 upstream) : NEURL1B (59748 downstream)																							GAAAGGTGCCAAAAACCACAG	0.527													6	3	---	---	---	---	
GFPT2	9945	broad.mit.edu	37	5	179746751	179746751	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179746751delA	uc003mlw.1	-							NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	tagtcttgccaaaaaaaatca	0.134													4	2	---	---	---	---	
SLC22A23	63027	broad.mit.edu	37	6	3422563	3422564	+	Intron	DEL	AC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3422563_3422564delAC	uc003mvm.3	-						SLC22A23_uc003mvn.3_Intron|SLC22A23_uc003mvo.3_Intron|SLC22A23_uc003mvp.1_Intron|SLC22A23_uc010jnn.2_Intron|SLC22A23_uc010jno.2_Intron	NM_015482	NP_056297	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				AATGGCAAGAACACACACACAG	0.460													4	2	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	21944457	21944457	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21944457delG	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron|FLJ22536_uc011djj.1_Intron|FLJ22536_uc003ndk.1_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						CTTCAGTCATGGGTCCTCAAG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26570861	26570862	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26570861_26570862insA	uc003nih.2	+											Homo sapiens cDNA clone IMAGE:4838711.																		GCAGCAGACCCCCCCACCCCAC	0.436													4	2	---	---	---	---	
HLA-DQB2	3120	broad.mit.edu	37	6	32726935	32726936	+	Intron	DEL	AT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32726935_32726936delAT	uc003oby.3	-						HLA-DQB2_uc003obz.2_Intron	NR_003937		Q5SR06	Q5SR06_HUMAN	SubName: Full=Major histocompatibility complex, class II, DQ beta 2; SubName: Full=Putative uncharacterized protein ENSP00000372579;						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	integral to membrane|MHC class II protein complex					0						ACAGGGAAAGATATAGGAGTGA	0.540													4	2	---	---	---	---	
TFEB	7942	broad.mit.edu	37	6	41673473	41673473	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41673473delC	uc003oqs.1	-						TFEB_uc003oqt.1_Intron|TFEB_uc003oqu.1_Intron|TFEB_uc003oqv.1_Intron|TFEB_uc010jxo.1_Intron|TFEB_uc003oqx.1_Intron|TFEB_uc003oqy.1_Intron|TFEB_uc003oqz.1_Intron|TFEB_uc010jxq.1_Intron|TFEB_uc003oqw.1_5'UTR|TFEB_uc010jxp.1_Intron	NM_007162	NP_009093	P19484	TFEB_HUMAN	transcription factor EB						embryonic placenta development|humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			AATCATGGGGCCAGAATCCCA	0.552			T	ALPHA	renal (childhood epithelioid)						OREG0017433	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77259187	77259187	+	IGR	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77259187delC								IMPG1 (476852 upstream) : HTR1B (912761 downstream)																							cctctggtctccaccttacca	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134845337	134845337	+	IGR	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134845337delG								SGK1 (206141 upstream) : ALDH8A1 (393192 downstream)																							ATGACTGCCTGGACATGCTGA	0.438													4	2	---	---	---	---	
NHSL1	57224	broad.mit.edu	37	6	138886237	138886237	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138886237delG	uc003qhx.2	-							NM_020464	NP_065197	Q5SYE7	NHSL1_HUMAN	NHS-like 1 isoform 1												0						ttgtttttgtgggtttttctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	144522213	144522213	+	IGR	DEL	A	-	-	rs10782292	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144522213delA								STX11 (9138 upstream) : UTRN (85277 downstream)																							GCGAGCGGGGAAAAAAAAAAG	0.418													4	4	---	---	---	---	
TMEM184A	202915	broad.mit.edu	37	7	1587599	1587599	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1587599delC	uc003skv.3	-						TMEM184A_uc003skt.3_Intron|TMEM184A_uc003skw.3_Intron	NM_001097620	NP_001091089	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A							integral to membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		GGCCGCTCAGCCCCAGCCCCA	0.721													4	2	---	---	---	---	
DGKB	1607	broad.mit.edu	37	7	14867545	14867545	+	Intron	DEL	C	-	-	rs35197364		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14867545delC	uc003ssz.2	-						DGKB_uc011jxt.1_Intron|DGKB_uc003sta.2_Intron|DGKB_uc011jxu.1_Intron|DGKB_uc011jxv.1_Intron	NM_004080	NP_004071	Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)	AATATGAACTCCGAAATGAAT	0.403													1	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23603688	23603688	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23603688delT								TRA2A (32032 upstream) : CLK2P (20647 downstream)																							CAAAGGGGCATTTCTTAATAC	0.373													331	188	---	---	---	---	
MPP6	51678	broad.mit.edu	37	7	24708363	24708363	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24708363delT	uc003swx.2	+						MPP6_uc003swy.2_Intron|MPP6_uc010kur.2_Intron	NM_016447	NP_057531	Q9NZW5	MPP6_HUMAN	membrane protein, palmitoylated 6						protein complex assembly		protein binding				0						TTATCATTAGTTATTGTTATT	0.353													31	17	---	---	---	---	
LOC402644	402644	broad.mit.edu	37	7	28319476	28319476	+	5'Flank	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28319476delT	uc010kuz.1	-							NM_001126493	NP_001119965			hypothetical protein LOC402644												0						TTTGTTTTTATTTTTTTCTGT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37510642	37510643	+	IGR	INS	-	ATA	ATA	rs74456953		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37510642_37510643insATA								ELMO1 (22112 upstream) : GPR141 (269353 downstream)																							TAAGCGTTGTCATGACTGTGCA	0.460													6	6	---	---	---	---	
LOC285954	285954	broad.mit.edu	37	7	41797976	41797976	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41797976delT	uc003tht.3	+							NR_027118				Homo sapiens cDNA FLJ38947 fis, clone NT2NE2017792.												0						taaacactgattttttttttc	0.000													12	8	---	---	---	---	
SPDYE1	285955	broad.mit.edu	37	7	44044972	44044974	+	Intron	DEL	TGT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44044972_44044974delTGT	uc003tjf.2	+						POLR2J4_uc003tjc.2_Intron|POLR2J4_uc003tjd.2_Intron|POLR2J4_uc010kxw.2_Intron|POLR2J4_uc003tje.3_Intron|uc003tjg.1_Intron	NM_175064	NP_778234	Q8NFV5	SPDE1_HUMAN	Williams Beuren syndrome chromosome region 19											ovary(1)	1						TATCATAGACTGTTGTTTCTAAA	0.232													7	4	---	---	---	---	
CCT6A	908	broad.mit.edu	37	7	56130682	56130682	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56130682delA	uc003trl.1	+						PSPH_uc003trj.2_Intron|CCT6A_uc003trm.1_Intron|CCT6A_uc011kcu.1_Intron|SUMF2_uc003tro.2_5'Flank|SUMF2_uc011kcv.1_5'Flank|SUMF2_uc011kcw.1_5'Flank|SUMF2_uc011kcx.1_5'Flank|SUMF2_uc003trv.2_5'Flank|SUMF2_uc003trt.2_5'Flank|SUMF2_uc011kcy.1_5'Flank|SUMF2_uc011kcz.1_5'Flank|SUMF2_uc003tru.2_5'Flank|SUMF2_uc011kda.1_5'Flank|SUMF2_uc003trx.2_5'Flank	NM_001762	NP_001753	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A isoform						'de novo' posttranslational protein folding	cytosol	ATP binding|unfolded protein binding			upper_aerodigestive_tract(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CATCTGAGCCATCTTATTTTT	0.443													210	119	---	---	---	---	
TYW1	55253	broad.mit.edu	37	7	66532750	66532751	+	Intron	INS	-	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66532750_66532751insT	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)				ACATTGTTTTCTTTTTTTTCTA	0.282													4	2	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101559309	101559310	+	Intron	INS	-	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101559309_101559310insG	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						TCTCTCCCCCAGTGTTCTGGTC	0.510													23	19	---	---	---	---	
DPY19L2P2	349152	broad.mit.edu	37	7	102920300	102920300	+	5'UTR	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102920300delG	uc003vbh.3	-	2					DPY19L2P2_uc003vbg.3_Intron|DPY19L2P2_uc010lit.2_Intron|DPY19L2P2_uc003vbi.2_Frame_Shift_Del_p.P100fs|DPY19L2P2_uc003vbj.2_Frame_Shift_Del_p.P100fs	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						TGGTTCTGCTGGGGAACCACC	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136711520	136711521	+	Intron	DEL	TG	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136711520_136711521delTG	uc003vtp.1	-											Homo sapiens clone N1 NTera2D1 teratocarcinoma mRNA.																		CGCTGGCCTCTGTCTCATTTCA	0.262													4	2	---	---	---	---	
AGK	55750	broad.mit.edu	37	7	141348830	141348830	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141348830delA	uc003vwi.2	+						AGK_uc011krg.1_Intron	NM_018238	NP_060708	Q53H12	AGK_HUMAN	acylglycerol kinase precursor						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)					CTTATGTAGTAAAAAAAAAAG	0.333													4	2	---	---	---	---	
KEL	3792	broad.mit.edu	37	7	142654701	142654701	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142654701delT	uc003wcb.2	-							NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase						proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					CCAGGCCTACTTCTGTCTTCC	0.299													3	3	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3509639	3509640	+	Intron	INS	-	ACC	ACC	rs141532900	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3509639_3509640insACC	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		tcagcacgcttaccatcagagc	0.074													2	5	---	---	---	---	
FAM167A	83648	broad.mit.edu	37	8	11315592	11315593	+	Intron	INS	-	AGA	AGA	rs149814770	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11315592_11315593insAGA	uc003wtw.2	-							NM_053279	NP_444509	Q96KS9	F167A_HUMAN	hypothetical protein LOC83648												0						ATCTCCCCAGCAGACCTCCCAC	0.450													11	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20274633	20274633	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20274633delT								LZTS1 (161830 upstream) : None (None downstream)																							ATCATGGTTATTTTTTTTTGG	0.383													4	2	---	---	---	---	
INTS9	55756	broad.mit.edu	37	8	28692567	28692568	+	Intron	DEL	CT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28692567_28692568delCT	uc003xha.2	-						INTS9_uc011lav.1_Intron|INTS9_uc011law.1_Intron|INTS9_uc011lax.1_Intron|INTS9_uc010lvc.2_Intron|INTS9_uc003xhb.2_Intron	NM_018250	NP_060720	Q9NV88	INT9_HUMAN	integrator complex subunit 9 isoform 1						snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		ttccattaaactttgaccacct	0.000													5	3	---	---	---	---	
AGPAT6	137964	broad.mit.edu	37	8	41468547	41468547	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41468547delA	uc003xnz.2	+							NM_178819	NP_848934	Q86UL3	GPAT4_HUMAN	lysophosphatidic acid acyltransferase zeta						acyl-CoA metabolic process|lactation|phosphatidylcholine biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	glycerol-3-phosphate O-acyltransferase activity				0	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			ggagtttgagaccagcctggc	0.030													10	10	---	---	---	---	
PDE7A	5150	broad.mit.edu	37	8	66637441	66637441	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66637441delA	uc003xvq.2	-						PDE7A_uc003xvr.2_Intron|PDE7A_uc003xvp.2_Intron	NM_002604	NP_002595	Q13946	PDE7A_HUMAN	phosphodiesterase 7A isoform b							cell fraction|cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding				0			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Dyphylline(DB00651)|Ketotifen(DB00920)	TATTTGCTTTAAAAAAAAAAT	0.338													3	4	---	---	---	---	
SLCO5A1	81796	broad.mit.edu	37	8	70589142	70589142	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70589142delA	uc003xyl.2	-						SLCO5A1_uc010lzb.2_Intron|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.2_Intron	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,							integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			TTGTTTCTACAAAAATACTGG	0.353													4	2	---	---	---	---	
ZNF704	619279	broad.mit.edu	37	8	81587754	81587754	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81587754delA	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)			aaacaaatgtaatcaccagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	86529394	86529394	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86529394delA								CA2 (135673 upstream) : REXO1L1 (39170 downstream)																							TCGACAAGGCAAAAAAAAAAC	0.224													4	2	---	---	---	---	
DPY19L4	286148	broad.mit.edu	37	8	95778604	95778604	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95778604delA	uc003ygx.2	+							NM_181787	NP_861452	Q7Z388	D19L4_HUMAN	dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)					actctgtctcaaaaaaaaaga	0.149													5	3	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	97847024	97847025	+	Intron	DEL	TT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97847024_97847025delTT	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					TTTCACTCTCTTGGGAAGTTGG	0.361													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134987031	134987031	+	IGR	DEL	T	-	-	rs112711998		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134987031delT								ST3GAL1 (402848 upstream) : ZFAT (503002 downstream)																							ccttacaggcttttttttttt	0.020													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143094637	143094639	+	IGR	DEL	ATC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143094637_143094639delATC								MIR1302-7 (226963 upstream) : NCRNA00051 (185078 downstream)																							tgtcatcactatcatcatcatca	0.246													4	2	---	---	---	---	
JRK	8629	broad.mit.edu	37	8	143750582	143750607	+	Intron	DEL	GTGTGTGTGTGTGTGTGTGTGTGTGT	-	-	rs143513469	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143750582_143750607delGTGTGTGTGTGTGTGTGTGTGTGTGT	uc003ywo.2	-						JRK_uc003ywp.2_Intron|JRK_uc010mew.1_5'Flank	NM_001077527	NP_001070995			jerky isoform b												0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				CAGGGGCATAgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt	0.460											OREG0019038	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
BAG1	573	broad.mit.edu	37	9	33263782	33263782	+	Intron	DEL	C	-	-	rs3834388		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33263782delC	uc003zsj.2	-						SUGT1P1_uc010mjq.1_Intron|BAG1_uc003zsi.2_Intron|BAG1_uc003zsk.2_Intron|CHMP5_uc003zsl.3_5'Flank|CHMP5_uc003zsm.3_5'Flank|CHMP5_uc011lnv.1_5'Flank	NM_004323	NP_004314	Q99933	BAG1_HUMAN	BCL2-associated athanogene isoform 1L						anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway|chaperone cofactor-dependent protein refolding	cytoplasm|intermediate filament cytoskeleton|nucleus	protein binding|receptor signaling protein activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)			CAGAGTACAACGCTTGGACCC	0.562													6	3	---	---	---	---	
MCART1	92014	broad.mit.edu	37	9	37886397	37886397	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37886397delT	uc004aar.1	-						MCART1_uc004aaq.1_Intron|uc004aat.1_5'Flank	NR_024873		Q9H1U9	MCAR1_HUMAN	Homo sapiens cDNA FLJ34088 fis, clone FCBBF3005698.						transport	integral to membrane|mitochondrial inner membrane				ovary(2)|breast(1)	3				GBM - Glioblastoma multiforme(29;0.00559)|Lung(182;0.0422)		AGATCCTCACTTTGGCAGTGC	0.483													93	50	---	---	---	---	
LOC653501	653501	broad.mit.edu	37	9	39461895	39461895	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39461895delA	uc010mmh.2	-						LOC653501_uc004abo.3_Intron	NR_003528				RecName: Full=Zinc finger protein 658B;												0						TCATGTGCCTAAAAAAAAAAT	0.254													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68419453	68419454	+	IGR	DEL	AA	-	-	rs62545511		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68419453_68419454delAA								FAM27B (625264 upstream) : MIR1299 (582785 downstream)																							catacacaccaaacacacatac	0.000													4	2	---	---	---	---	
KIAA1958	158405	broad.mit.edu	37	9	115398849	115398850	+	Intron	INS	-	AC	AC			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115398849_115398850insAC	uc004bgf.1	+						KIAA1958_uc011lwx.1_Intron	NM_133465	NP_597722	Q8N8K9	K1958_HUMAN	hypothetical protein LOC158405											skin(1)	1						atcagatccatacaaaaatcta	0.000													229	120	---	---	---	---	
PPP6C	5537	broad.mit.edu	37	9	127913971	127913972	+	Intron	DEL	GT	-	-	rs73668905	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127913971_127913972delGT	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2						GCTTGCTCCAGTGTAGCTTTCT	0.416													8	4	---	---	---	---	
TOR2A	27433	broad.mit.edu	37	9	130494778	130494778	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130494778delG	uc004brs.3	-						TOR2A_uc004brt.3_Intron|TOR2A_uc004brw.3_3'UTR|TOR2A_uc011maj.1_3'UTR|TOR2A_uc004bru.3_Intron|TOR2A_uc004brv.3_Intron|TOR2A_uc004brx.1_Frame_Shift_Del_p.P100fs	NM_001085347	NP_001078816	Q5JU69	TOR2A_HUMAN	torsin family 2, member A isoform a						chaperone mediated protein folding requiring cofactor	endoplasmic reticulum|extracellular region	ATP binding|nucleoside-triphosphatase activity				0						ATGAGACCCCGGGAGAGCCTG	0.433													4	2	---	---	---	---	
SURF2	6835	broad.mit.edu	37	9	136227641	136227641	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136227641delT	uc004cdi.2	+							NM_017503	NP_059973	Q15527	SURF2_HUMAN	surfeit 2								protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;4.87e-07)|Epithelial(140;4.02e-06)|all cancers(34;3.71e-05)		CACCTTTGCCTTTGCCATCAG	0.537													4	2	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140615677	140615677	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140615677delC	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		CTCACACTCACCCCTCCCAGA	0.303													3	3	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140615681	140615681	+	Intron	DEL	T	-	-	rs72444209		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140615681delT	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		CACTCACCCCTCCCAGACTTc	0.303													4	2	---	---	---	---	
LARP4B	23185	broad.mit.edu	37	10	903262	903262	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:903262delA	uc001ifs.1	-							NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3						aaggagggggaaaaaaactgt	0.025													5	3	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1552223	1552226	+	Intron	DEL	TCTT	-	-	rs10567053		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1552223_1552226delTCTT	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		ttcttttttctctttctttctttt	0.113													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10701905	10701906	+	IGR	DEL	AG	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10701905_10701906delAG								None (None upstream) : SFTA1P (124496 downstream)																							cacaagggtcagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10775400	10775400	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10775400delA								None (None upstream) : SFTA1P (51002 downstream)																							GGAGGTAGTGAAAAAAAAAAG	0.413													16	8	---	---	---	---	
UPF2	26019	broad.mit.edu	37	10	12009639	12009639	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12009639delC	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron|UPF2_uc009xiz.1_Intron	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				acctccgcctcctgggttcaa	0.020													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12832145	12832146	+	Intron	INS	-	C	C			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12832145_12832146insC	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		GCAAGCCCAAGCCCCCAGCATG	0.450													4	2	---	---	---	---	
ARHGAP21	57584	broad.mit.edu	37	10	24939895	24939895	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24939895delA	uc001isb.2	-						ARHGAP21_uc009xkl.1_Intron|ARHGAP21_uc001isc.1_Intron|ARHGAP21_uc001isd.1_Intron	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21						signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8						ctgaggagacaaaaaaaaaaa	0.000													4	3	---	---	---	---	
GJD4	219770	broad.mit.edu	37	10	35894216	35894216	+	5'Flank	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35894216delC	uc001iyy.1	+							NM_153368	NP_699199	Q96KN9	CXD4_HUMAN	connexin40.1						cell communication	connexon complex|integral to membrane				large_intestine(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						CCGGGAATATCCCAGGCGAGT	0.493													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53004250	53004252	+	Intron	DEL	CCT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53004250_53004252delCCT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		ACACACTCTGCCTCCTCCTCCCA	0.438													4	2	---	---	---	---	
FAM149B1	317662	broad.mit.edu	37	10	74953008	74953008	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74953008delT	uc009xqz.2	+						FAM149B1_uc010qkf.1_Intron|FAM149B1_uc001jtq.2_Intron	NM_173348	NP_775483	Q96BN6	F149B_HUMAN	hypothetical protein LOC317662												0						ATTTCTTGTATTTTTTTTTTT	0.363													6	3	---	---	---	---	
TMEM180	79847	broad.mit.edu	37	10	104221895	104221895	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104221895delC	uc001kvt.2	+						TMEM180_uc001kvs.2_Intron|TMEM180_uc010qql.1_Intron|TMEM180_uc010qqm.1_Intron	NM_024789	NP_079065	Q14CX5	TM180_HUMAN	transmembrane protein 180							integral to membrane				ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GGAGGATGGGCCCCCACCCCC	0.597													4	2	---	---	---	---	
PDCD11	22984	broad.mit.edu	37	10	105178005	105178011	+	Intron	DEL	ACCCATG	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105178005_105178011delACCCATG	uc001kwy.1	+							NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11						mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CGATGGGTCCACCCATGAGTCCTGGTG	0.594													20	11	---	---	---	---	
ATE1	11101	broad.mit.edu	37	10	123673585	123673585	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123673585delT	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2						protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				agttaagagattttttttttc	0.055													5	3	---	---	---	---	
STK32C	282974	broad.mit.edu	37	10	134077475	134077475	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134077475delA	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_Intron|STK32C_uc009ybd.1_Intron	NM_173575	NP_775846	Q86UX6	ST32C_HUMAN	serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		gcgccaggtgaaggcagccag	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	3454865	3454886	+	IGR	DEL	TATATATATATATATATATATA	-	-	rs56325013		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3454865_3454886delTATATATATATATATATATATA								LOC650368 (24487 upstream) : TRPC2 (183576 downstream)																							tgtgtgtatgtatatatatatatatatatatatatatatata	0.000													5	4	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21097968	21097968	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21097968delA	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						AGTGACCTGGAAATAGTACAT	0.418													4	2	---	---	---	---	
CAT	847	broad.mit.edu	37	11	34489777	34489777	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34489777delT	uc001mvm.2	+						CAT_uc001mvn.2_Intron	NM_001752	NP_001743	P04040	CATA_HUMAN	catalase						hydrogen peroxide catabolic process|negative regulation of apoptosis|positive regulation of cell division|protein tetramerization|purine base metabolic process|purine nucleotide catabolic process|UV protection	peroxisomal matrix|peroxisomal membrane	catalase activity|heme binding|NADP binding|protein homodimerization activity			ovary(2)|pancreas(1)	3		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	AGTAGGTGAATTTTGTTGGTG	0.348													33	15	---	---	---	---	
VWCE	220001	broad.mit.edu	37	11	61040562	61040563	+	Intron	DEL	AC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61040562_61040563delAC	uc001nra.2	-						VWCE_uc001nrb.2_Intron	NM_152718	NP_689931	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains							extracellular region	calcium ion binding			ovary(1)	1						agacacatgtacacacacacac	0.238													5	3	---	---	---	---	
RPLP0P2	113157	broad.mit.edu	37	11	61405252	61405252	+	3'UTR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61405252delA	uc001nrz.1	+	5						NR_002775				SubName: Full=cDNA FLJ51469, highly similar to 60S acidic ribosomal protein P0;												0						gaaagaaaagaaaaaaaaaat	0.129													4	2	---	---	---	---	
ASRGL1	80150	broad.mit.edu	37	11	62140935	62140935	+	Intron	DEL	T	-	-	rs112856978		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62140935delT	uc001nte.3	+						ASRGL1_uc001ntf.3_Intron|ASRGL1_uc001ntg.3_Intron|ASRGL1_uc001nth.1_Intron	NM_025080	NP_079356	Q7L266	ASGL1_HUMAN	asparaginase-like 1						asparagine catabolic process via L-aspartate|protein maturation	cytoplasm|microtubule cytoskeleton|nucleus	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	AATCTAGGTGTTTTTTTTTTC	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74209274	74209274	+	3'UTR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74209274delT	uc001ove.2	+	2										SubName: Full=Similar to Cytochrome c, somatic;																		gaatacactatttttttcgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107764155	107764155	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107764155delT								SLC35F2 (34241 upstream) : RAB39 (35122 downstream)																							AGATTTGAGGTTTTTTTTTGG	0.393													4	2	---	---	---	---	
ATM	472	broad.mit.edu	37	11	108200141	108200141	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108200141delT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkg.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		ttgttttttgttttttttttt	0.149			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			4	2	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126589891	126589891	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126589891delA	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		gctcctactcatccccctttg	0.000													4	2	---	---	---	---	
MFAP5	8076	broad.mit.edu	37	12	8804492	8804492	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8804492delT	uc001qut.1	-						MFAP5_uc001qus.2_Intron|MFAP5_uc009zge.1_Intron	NM_003480	NP_003471	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5 precursor							microfibril	extracellular matrix structural constituent			breast(1)	1	Lung SC(5;0.184)					CAGGATGGGATTTTTTTCCTT	0.348													4	2	---	---	---	---	
CLEC1A	51267	broad.mit.edu	37	12	10225700	10225701	+	Intron	DEL	AC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10225700_10225701delAC	uc001qxb.2	-						CLEC1A_uc009zhf.2_Intron|CLEC1A_uc001qxc.2_Intron|CLEC1A_uc001qxd.2_Intron|CLEC1A_uc010sgx.1_Intron	NM_016511	NP_057595	Q8NC01	CLC1A_HUMAN	C-type lectin-like receptor-1						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane|intracellular	sugar binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2						AAACGAACAAACACACACACAC	0.223													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	14392789	14392789	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14392789delA								GRIN2B (259767 upstream) : ATF7IP (125822 downstream)																							AACGTTTTCTAAAAGGGGGCG	0.358													4	2	---	---	---	---	
PLCZ1	89869	broad.mit.edu	37	12	18852630	18852641	+	Intron	DEL	GAATATACATTT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18852630_18852641delGAATATACATTT	uc010sid.1	-						PLCZ1_uc001rdv.3_Intron|PLCZ1_uc001rdw.3_Intron|PLCZ1_uc001rdu.1_Intron|PLCZ1_uc009zil.1_Intron	NM_033123	NP_149114	Q86YW0	PLCZ1_HUMAN	phospholipase C, zeta 1						intracellular signal transduction|lipid catabolic process|multicellular organismal development	nucleus|perinuclear region of cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					AATTTTATGAGAATATACATTTTATAAATATC	0.278													23	10	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	21008396	21008397	+	Intron	DEL	CT	-	-	rs35308450		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21008396_21008397delCT	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					tgttgaaaaactctgGTCCTAC	0.208													2	4	---	---	---	---	
OVCH1	341350	broad.mit.edu	37	12	29586943	29586943	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29586943delG	uc001rix.1	-							NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TAAATATAATGGCAAATGTTT	0.328													4	3	---	---	---	---	
HDAC7	51564	broad.mit.edu	37	12	48190210	48190210	+	Intron	DEL	T	-	-	rs72050864		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48190210delT	uc009zkv.1	-						HDAC7_uc001rqe.2_5'Flank|HDAC7_uc010slo.1_Intron|HDAC7_uc001rqj.3_Intron|HDAC7_uc001rqk.3_Intron			Q8WUI4	HDAC7_HUMAN	Synthetic construct DNA, clone: pF1KB0470, Homo sapiens HDAC7 gene for histone deacetylase 7, without stop codon, in Flexi system.						negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)		TCCTGCtttcttttttttttt	0.318													3	3	---	---	---	---	
AMHR2	269	broad.mit.edu	37	12	53818668	53818668	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53818668delT	uc001scx.1	+	3	486	c.408delT	c.(406-408)GGTfs	p.G136fs	AMHR2_uc009zmy.1_Frame_Shift_Del_p.G136fs	NM_020547	NP_065434	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II isoform	136	Extracellular (Potential).				Mullerian duct regression		ATP binding|hormone binding|metal ion binding			ovary(1)|skin(1)	2					Adenosine triphosphate(DB00171)	GCTCCCAGGGTCCCCAGGCTG	0.627									Persistant_Mullerian_Duct_Syndrome_(type_I_and_II)				24	12	---	---	---	---	
BAZ2A	11176	broad.mit.edu	37	12	57030309	57030309	+	5'Flank	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57030309delG	uc001slq.1	-						BAZ2A_uc010sqr.1_5'Flank	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0						GGCCGGCAAAGGGGGAAGGAA	0.537											OREG0021927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PTPRB	5787	broad.mit.edu	37	12	71031381	71031382	+	5'Flank	DEL	TT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71031381_71031382delTT	uc001swc.3	-						PTPRB_uc001swa.3_5'Flank|PTPRB_uc001swd.3_5'Flank|PTPRB_uc009zrr.1_5'Flank|PTPRB_uc001swe.2_5'Flank	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B						angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TGATTACCTCTTTTTTTTAATG	0.391													4	2	---	---	---	---	
TMEM19	55266	broad.mit.edu	37	12	72091466	72091466	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72091466delT	uc001sws.2	+						TMEM19_uc001swr.1_Intron|TMEM19_uc009zru.1_Intron	NM_018279	NP_060749	Q96HH6	TMM19_HUMAN	transmembrane protein 19							integral to membrane					0		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)		AATTGGAAAATTTCTGTCGAC	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91665256	91665260	+	IGR	DEL	AGTGG	-	-	rs142263771		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91665256_91665260delAGTGG								DCN (88450 upstream) : BTG1 (713606 downstream)																							agtccaaggtagtggagtggcgttg	0.000													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110047731	110047732	+	IGR	INS	-	G	G	rs149101671	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110047731_110047732insG								MVK (12661 upstream) : C12orf34 (104458 downstream)																							TGATAAATGGAGGGGCAGGGGG	0.530													7	4	---	---	---	---	
PRKAB1	5564	broad.mit.edu	37	12	120110460	120110461	+	Intron	DEL	AG	-	-	rs150497180		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120110460_120110461delAG	uc009zwu.2	+						PRKAB1_uc001txg.2_Intron	NM_006253	NP_006244	Q9Y478	AAKB1_HUMAN	AMP-activated protein kinase beta 1						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol					0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Adenosine monophosphate(DB00131)|Metformin(DB00331)	TACAGAAGAAAGAGAATATTTC	0.342													9	8	---	---	---	---	
BCL7A	605	broad.mit.edu	37	12	122481799	122481799	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122481799delC	uc001ubp.2	+	4	416	c.279delC	c.(277-279)AACfs	p.N93fs	BCL7A_uc001ubo.2_Frame_Shift_Del_p.N93fs	NM_001024808	NP_001019979	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A isoform b	93					negative regulation of transcription, DNA-dependent					ovary(1)|lung(1)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		CAGACGATAACAGCAACCAGA	0.602			T	MYC	BNHL								105	50	---	---	---	---	
ATP8A2	51761	broad.mit.edu	37	13	26535512	26535512	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26535512delA	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TAGAAGAATGAAAGTAAGAAG	0.493													7	4	---	---	---	---	
ENOX1	55068	broad.mit.edu	37	13	43898886	43898887	+	Intron	INS	-	T	T	rs150111341	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43898886_43898887insT	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron|ENOX1_uc001uyz.3_Intron|ENOX1_uc010tfm.1_Intron	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		AGCAAGCAGGCTCCTTAGACCT	0.545													4	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	97700255	97700256	+	IGR	DEL	AC	-	-	rs61356507		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97700255_97700256delAC								OXGR1 (53651 upstream) : MBNL2 (174318 downstream)																							tcaaaaaaaaacaaaaacaaaa	0.054													5	3	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109777451	109777452	+	Intron	INS	-	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109777451_109777452insT	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc010tjh.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)			CATGATCCTTCTATAAAAGTTA	0.366													83	47	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	109860719	109860719	+	IGR	DEL	A	-	-	rs35569790		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109860719delA								MYO16 (364 upstream) : IRS2 (545467 downstream)																							atcagcaggcatagaactgac	0.000													3	4	---	---	---	---	
ATP11A	23250	broad.mit.edu	37	13	113490618	113490619	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113490618_113490619insA	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|ATP11A_uc001vsm.1_Intron	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				GGTTGTGTTTTATTCTGATGAC	0.282													77	53	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	25827413	25827414	+	IGR	INS	-	CTCTC	CTCTC	rs71121825		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25827413_25827414insCTCTC								STXBP6 (308242 upstream) : None (None downstream)																							TCTCTCTCTCTTTTTTTTTTTT	0.450													8	5	---	---	---	---	
HECTD1	25831	broad.mit.edu	37	14	31606025	31606025	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31606025delT	uc001wrc.1	-						HECTD1_uc001wrd.1_Intron	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TCAAAGAttcttttttttttt	0.114													7	4	---	---	---	---	
RALGAPA1	253959	broad.mit.edu	37	14	36096150	36096150	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36096150delA	uc001wti.2	-						RALGAPA1_uc010amp.2_Intron|RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						CAGTGGTCTCAAAAAAAAATC	0.264													3	4	---	---	---	---	
SIP1	8487	broad.mit.edu	37	14	39602636	39602636	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39602636delT	uc001wuq.2	+						SIP1_uc001wur.2_Intron|SIP1_uc001wus.2_Intron|SIP1_uc010amx.2_Intron	NM_003616	NP_003607	O14893	GEMI2_HUMAN	SMN-interacting protein 1 isoform alpha						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)		TCCCTCTTTATTTTTTTTTCC	0.353													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49005976	49005976	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49005976delT								MDGA2 (861988 upstream) : None (None downstream)																							tcacccttaattttttatgtc	0.000													4	2	---	---	---	---	
SLC39A9	55334	broad.mit.edu	37	14	69865202	69865202	+	5'Flank	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69865202delT	uc001xle.2	+						ERH_uc001xlc.2_5'Flank|SLC39A9_uc001xld.3_5'Flank|SLC39A9_uc010aqx.2_5'Flank|SLC39A9_uc001xlf.3_5'Flank|SLC39A9_uc001xlg.3_5'Flank	NM_018375	NP_060845	Q9NUM3	S39A9_HUMAN	solute carrier family 39 (zinc transporter),						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		GGAAGAATTATTTTTTTTCAA	0.418													6	3	---	---	---	---	
TECPR2	9895	broad.mit.edu	37	14	102891806	102891807	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102891806_102891807insA	uc001ylw.1	+						TECPR2_uc010awl.2_Intron|TECPR2_uc010txx.1_Intron	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2								protein binding			lung(1)|central_nervous_system(1)|skin(1)	3						TTATAGATTTGAAAAAAAAAAT	0.292													4	2	---	---	---	---	
CDC42BPB	9578	broad.mit.edu	37	14	103440619	103440622	+	Intron	DEL	ACAC	-	-	rs71927029		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103440619_103440622delACAC	uc001ymi.1	-							NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta						actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		TTTTTTACTTacacacacacacac	0.299													4	2	---	---	---	---	
FAM7A3	89837	broad.mit.edu	37	15	32693850	32693851	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32693850_32693851insA	uc001zgb.2	-											Homo sapiens family with sequence similarity 7, member A3, mRNA (cDNA clone IMAGE:4579054).												0						ATCATGGCTAGAAAAAAAAAAA	0.391													15	16	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	34156100	34156100	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34156100delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TCTTACTTAGTTCAAGGTATA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	34691244	34691245	+	IGR	INS	-	A	A	rs138144152	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34691244_34691245insA								GOLGA8A (9243 upstream) : GOLGA8B (126240 downstream)																							TAGGAGCTATGAAAAAAAAAAC	0.342													6	5	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40897062	40897062	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40897062delT	uc010bbs.1	+						CASC5_uc010ucq.1_Intron|CASC5_uc001zme.2_Intron|CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TTATTATACCTCTATAAATAT	0.244													8	9	---	---	---	---	
TLN2	83660	broad.mit.edu	37	15	63014438	63014438	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63014438delT	uc002alb.3	+							NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						TTAATATTCCTTTTTTTTAGG	0.418													4	2	---	---	---	---	
RBPMS2	348093	broad.mit.edu	37	15	65055095	65055095	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65055095delA	uc002anq.2	-						MIR1272_hsa-mir-1272|MI0006408_5'Flank	NM_194272	NP_919248	Q6ZRY4	RBPS2_HUMAN	RNA binding protein with multiple splicing 2								nucleic acid binding|nucleotide binding				0						CAGAGAAGAGAAGGGGACAAG	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95551440	95551440	+	IGR	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95551440delG								MCTP2 (524260 upstream) : LOC145820 (424882 downstream)																							GTACAAGTTAGGGGAAAGGCC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97397783	97397783	+	IGR	DEL	T	-	-	rs35460526		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97397783delT								SPATA8 (68939 upstream) : LOC91948 (888063 downstream)																							ttttgtgccattttttttttt	0.000													4	4	---	---	---	---	
LRRC28	123355	broad.mit.edu	37	15	99873885	99873885	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99873885delT	uc002bva.1	+						LRRC28_uc010urs.1_Intron|LRRC28_uc002bvb.1_Intron|LRRC28_uc010urt.1_Intron|LRRC28_uc002bvc.1_Intron|LRRC28_uc010uru.1_Intron|LRRC28_uc002bvd.1_Intron	NM_144598	NP_653199	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28												0	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			TTTGTGTCTCTTTTTTTCTCC	0.403													4	2	---	---	---	---	
HAGH	3029	broad.mit.edu	37	16	1867532	1867534	+	Intron	DEL	CCA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1867532_1867534delCCA	uc002cna.2	-						HAGH_uc002cmz.2_Intron|HAGH_uc010uvp.1_Intron|HAGH_uc002cnb.1_Intron	NM_005326	NP_005317	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase isoform 1						glutathione biosynthetic process	cytoplasm|mitochondrial matrix|mitochondrial matrix	hydroxyacylglutathione hydrolase activity|zinc ion binding			ovary(1)	1		Hepatocellular(780;0.00335)			Glutathione(DB00143)	GCCCCCAATCCCACCAACTGTGG	0.616													4	3	---	---	---	---	
ZNF263	10127	broad.mit.edu	37	16	3333550	3333551	+	5'UTR	DEL	TA	-	-	rs139235136		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3333550_3333551delTA	uc002cuq.2	+	1					ZNF263_uc010uww.1_Intron|ZNF263_uc002cup.2_5'UTR	NM_005741	NP_005732	O14978	ZN263_HUMAN	zinc finger protein 263						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(3)|ovary(1)	4						GTGGGTCCTCTATATAGGGTGA	0.663													4	2	---	---	---	---	
GRIN2A	2903	broad.mit.edu	37	16	10063108	10063109	+	Intron	DEL	CA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10063108_10063109delCA	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc010uyn.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)	CTACTGACatcacctccctttt	0.178													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12492571	12492571	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12492571delT	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						tttaaaaacattttttttttt	0.100													3	3	---	---	---	---	
MYH11	4629	broad.mit.edu	37	16	15854710	15854711	+	Intron	DEL	GA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15854710_15854711delGA	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002dea.1_Intron	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						GTATTTTGCTGAGAGGCAATGA	0.371			T	CBFB	AML								4	2	---	---	---	---	
SULT1A3	6818	broad.mit.edu	37	16	30211957	30211958	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30211957_30211958insA	uc002dxd.2	+						uc002dtf.2_Intron|SULT1A3_uc002dxf.2_Intron|SULT1A3_uc002dxi.2_Intron|SULT1A3_uc002dxj.2_Intron|SULT1A3_uc010vek.1_Intron|SULT1A3_uc002dxk.2_Intron|SULT1A3_uc010bzt.2_5'Flank	NM_177552	NP_808220	P50224	ST1A3_HUMAN	sulfotransferase family, cytosolic, 1A,						3'-phosphoadenosine 5'-phosphosulfate metabolic process|catecholamine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity				0						gactccatctcaaaaaaaaaaa	0.218													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32447192	32447193	+	IGR	INS	-	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32447192_32447193insT								HERC2P4 (283318 upstream) : TP53TG3B (237648 downstream)																							TTACTGAGTACTTTTTTTTTCT	0.282													8	6	---	---	---	---	
DDX19A	55308	broad.mit.edu	37	16	70351678	70351678	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70351678delA	uc002eys.2	+						DDX19B_uc010vly.1_Intron|DDX19B_uc010vlv.1_Intron|DDX19B_uc010vlw.1_Intron|DDX19B_uc002eyo.2_Intron|DDX19B_uc002eyp.2_Intron|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_Intron|DDX19B_uc010vlx.1_Intron|uc002eyt.2_Intron	NM_007242	NP_009173	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)				ctgtctcaacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
OSGIN1	29948	broad.mit.edu	37	16	83984579	83984580	+	Intron	DEL	CA	-	-	rs71392792		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83984579_83984580delCA	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron|OSGIN1_uc002fhc.2_5'Flank	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						tacatactggcacacacgtaca	0.000													1	8	---	---	---	---	
MBTPS1	8720	broad.mit.edu	37	16	84092781	84092782	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84092781_84092782insA	uc002fhi.2	-						MBTPS1_uc002fhh.2_Intron	NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1						cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2						ATAACTGTCGCAAATGACAAGC	0.381													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85604652	85604652	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85604652delT								FAM92B (458538 upstream) : KIAA0182 (40377 downstream)																							AGGAGAGTGGTTTTTATCTCA	0.169											OREG0032071	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86213728	86213729	+	IGR	INS	-	AC	AC			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86213728_86213729insAC								IRF8 (257519 upstream) : LOC732275 (151727 downstream)																							CTCTTCTGGTTacacacacata	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88312508	88312509	+	IGR	INS	-	ATT	ATT			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88312508_88312509insATT								BANP (201585 upstream) : ZNF469 (181370 downstream)																							GTGTAGATATCAGTGCACGGTT	0.530													4	2	---	---	---	---	
MYO1C	4641	broad.mit.edu	37	17	1377414	1377415	+	Intron	DEL	CA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1377414_1377415delCA	uc002fsp.2	-						MYO1C_uc002fsn.2_Intron|MYO1C_uc002fso.2_Intron|MYO1C_uc010vqj.1_Intron|MYO1C_uc010vqk.1_Intron	NM_001080779	NP_001074248	O00159	MYO1C_HUMAN	myosin IC isoform a						mRNA transport|protein transport|transmembrane transport	basal plasma membrane|cytoplasm|filamentous actin|lateral plasma membrane|nuclear pore|nucleolus|nucleoplasm|stereocilium membrane	actin binding|ATP binding|calmodulin binding|motor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ATAGACACAGCACACACACACA	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	8312283	8312284	+	IGR	DEL	CA	-	-	rs143690512		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8312283_8312284delCA								RNF222 (11139 upstream) : NDEL1 (26895 downstream)																							aacacacacgcacacacacaca	0.139													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21553361	21553361	+	IGR	DEL	C	-	-	rs75992433		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21553361delC								C17orf51 (75630 upstream) : FAM27L (272009 downstream)																							GCTACCTCCTCTCCTTTTCCT	0.294													8	6	---	---	---	---	
KRT13	3860	broad.mit.edu	37	17	39662027	39662028	+	5'Flank	INS	-	T	T	rs72133811		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39662027_39662028insT	uc002hwu.1	-						KRT13_uc002hwv.1_5'Flank|KRT13_uc002hww.2_5'Flank|KRT13_uc010wfr.1_5'Flank|KRT13_uc010cxo.2_5'Flank|KRT13_uc002hwx.1_5'Flank	NM_153490	NP_705694	P13646	K1C13_HUMAN	keratin 13 isoform a						epidermis development	intermediate filament	structural molecule activity			ovary(2)|skin(2)|pancreas(1)	5		Breast(137;0.000286)				TTGGGGGTGGCTTTTTTTTTAA	0.465													4	2	---	---	---	---	
DHX58	79132	broad.mit.edu	37	17	40258179	40258179	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40258179delA	uc002hyw.3	-						DHX58_uc002hyv.3_Intron|DHX58_uc010wgf.1_Intron	NM_024119	NP_077024	Q96C10	DHX58_HUMAN	RNA helicase LGP2						innate immune response	cytoplasm	ATP binding|DNA binding|helicase activity|protein binding|RNA binding|zinc ion binding				0		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		tctgtctgggaaaaaaaaaaa	0.010													4	2	---	---	---	---	
COPZ2	51226	broad.mit.edu	37	17	46110313	46110315	+	Intron	DEL	CTT	-	-	rs10563438		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46110313_46110315delCTT	uc002imy.2	-							NM_016429	NP_057513	Q9P299	COPZ2_HUMAN	coatomer protein complex, subunit zeta 2						intracellular protein transport|vesicle-mediated transport	cis-Golgi network|COPI vesicle coat					0						TGAGTGTATCCTTCTCTAGTTAT	0.478													4	6	---	---	---	---	
SAMD14	201191	broad.mit.edu	37	17	48191189	48191189	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48191189delG	uc002iqg.2	-						SAMD14_uc002iqd.2_Intron|SAMD14_uc002iqe.2_Intron|SAMD14_uc002iqf.2_Intron	NM_174920	NP_777580	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14												0						CAGCCCAGGAGGCTGGGCTGA	0.537													13	6	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64497079	64497079	+	Intron	DEL	T	-	-	rs71857011		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64497079delT	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	taaattaGGATTTTTTTTTTC	0.353													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5953179	5953179	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5953179delA								TMEM200C (61076 upstream) : L3MBTL4 (1527 downstream)																							GCATCAGGAGAAGGGGAAGGG	0.577													4	2	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13612656	13612657	+	Intron	INS	-	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13612656_13612657insG	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron|C18orf1_uc002kse.2_5'UTR|C18orf1_uc002ksf.2_5'UTR|C18orf1_uc002ksg.1_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)		GCTTTGAACGTGGGGGGGCTGC	0.559													96	43	---	---	---	---	
POTEC	388468	broad.mit.edu	37	18	14535288	14535288	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14535288delT	uc010dln.2	-						POTEC_uc010xaj.1_Intron	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2											skin(3)	3						Ttttggatgattttttttttc	0.184													9	5	---	---	---	---	
GREB1L	80000	broad.mit.edu	37	18	19032389	19032390	+	Intron	DEL	TG	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19032389_19032390delTG	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron|GREB1L_uc010xan.1_Intron|GREB1L_uc010dlr.1_Intron	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast							integral to membrane					0						TCTTCTGGAATGAAAATCAAAG	0.391													4	2	---	---	---	---	
TAF4B	6875	broad.mit.edu	37	18	23873647	23873648	+	Intron	INS	-	TC	TC			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23873647_23873648insTC	uc002kvu.3	+						TAF4B_uc002kvs.3_Intron|TAF4B_uc002kvt.3_Intron	NM_005640	NP_005631	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding						transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleolus|transcription factor TFIID complex	DNA binding|NF-kappaB binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)|skin(1)	3	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			aacaataaaatgcacaactatt	0.104													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27932975	27932975	+	IGR	DEL	A	-	-	rs35371290		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27932975delA								MIR302F (54049 upstream) : DSC3 (637078 downstream)																							tcacagtgagaaggtatgatg	0.000													2	4	---	---	---	---	
C18orf21	83608	broad.mit.edu	37	18	33558575	33558575	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33558575delA	uc002kzc.2	+						C18orf21_uc002kzd.2_Intron	NM_031446	NP_113634	Q32NC0	CR021_HUMAN	chromosome 18 open reading frame 21												0						ctccgtctccaaaaaaaaaaa	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	55431527	55431530	+	IGR	DEL	TTTC	-	-	rs12953732	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55431527_55431530delTTTC								ATP8B1 (32488 upstream) : NEDD4L (280089 downstream)																							tctttcttcttttcttccttcctt	0.167													9	4	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	55867238	55867239	+	Intron	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55867238_55867239insA	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						aagtctgaaacaaaaaagttta	0.134													4	2	---	---	---	---	
GNG7	2788	broad.mit.edu	37	19	2617180	2617180	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2617180delC	uc002lwd.2	-							NM_052847	NP_443079	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gcgtccctgacccccacccac	0.050													4	2	---	---	---	---	
AES	166	broad.mit.edu	37	19	3054430	3054430	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3054430delA	uc002lwy.1	-						AES_uc002lwx.1_3'UTR|AES_uc002lwz.1_Intron|AES_uc002lxa.1_Intron|AES_uc002lxb.1_Intron|AES_uc002lxc.2_Intron	NM_001130	NP_001121	Q08117	AES_HUMAN	amino-terminal enhancer of split isoform b						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of response to cytokine stimulus|negative regulation of transcription from RNA polymerase II promoter|organ morphogenesis|response to interleukin-1|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAAAACAATTAAAAGGGTTTT	0.478													4	2	---	---	---	---	
RYR1	6261	broad.mit.edu	37	19	38950306	38950307	+	Intron	INS	-	TGA	TGA	rs138474097	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38950306_38950307insTGA	uc002oit.2	+						RYR1_uc002oiu.2_Intron	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	ACTCCAGAATCTGATGATCTCA	0.500													3	5	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50752730	50752731	+	Intron	INS	-	GT	GT	rs146824061		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50752730_50752731insGT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		cctgtctctggctctgtcccct	0.000													7	4	---	---	---	---	
ZNF471	57573	broad.mit.edu	37	19	57019622	57019625	+	Intron	DEL	GACA	-	-	rs72265871		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57019622_57019625delGACA	uc002qnh.2	+							NM_020813	NP_065864	Q9BX82	ZN471_HUMAN	zinc finger protein 471						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		gtgtgtgtgtgACAGACCGAGAGT	0.495													4	2	---	---	---	---	
C20orf94	128710	broad.mit.edu	37	20	10518939	10518940	+	Intron	INS	-	C	C	rs151179526	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10518939_10518940insC	uc010zre.1	+							NM_001009608	NP_001009608	Q5VYV7	CT094_HUMAN	hypothetical protein LOC128710								protein binding				0						AAGGTTTTAGAcaaggtttctc	0.243													2	4	---	---	---	---	
KIF16B	55614	broad.mit.edu	37	20	16506655	16506658	+	Intron	DEL	ATAT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16506655_16506658delATAT	uc002wpg.1	-						KIF16B_uc010gch.1_Intron|KIF16B_uc010gci.1_Intron|KIF16B_uc010gcj.1_Intron	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						AATTGGCAAGATATTTTAAAGTAT	0.275													60	33	---	---	---	---	
DTD1	92675	broad.mit.edu	37	20	18708104	18708105	+	Intron	INS	-	C	C	rs140211273	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18708104_18708105insC	uc002wrf.3	+							NM_080820	NP_543010	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1						D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2						TGGGTGGACTTCTGTAACACCT	0.505													3	4	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19533801	19533801	+	Intron	DEL	G	-	-	rs3838379		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19533801delG	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						GCAGCTTACAGAACACAGGGC	0.149													4	2	---	---	---	---	
PIGU	128869	broad.mit.edu	37	20	33208614	33208614	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33208614delA	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron|PIGU_uc010gev.1_Intron	NM_080476	NP_536724	Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0						aaaaaaaaacaaaaaaaaaac	0.144													6	3	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	40784665	40784665	+	Intron	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40784665delC	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron|PTPRT_uc010ggi.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				catgcttcctcccaaaccgtt	0.090													4	2	---	---	---	---	
NTSR1	4923	broad.mit.edu	37	20	61369377	61369377	+	Intron	DEL	C	-	-	rs35251288		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61369377delC	uc002ydf.2	+							NM_002531	NP_002522	P30989	NTR1_HUMAN	neurotensin receptor 1							endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled			skin(2)|lung(1)|central_nervous_system(1)	4	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			TCCGCAACAGCCGCATCCCTT	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11149099	11149100	+	IGR	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11149099_11149100insA								BAGE (50162 upstream) : None (None downstream)																							gaagactccacaaaaactacta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	30274437	30274444	+	IGR	DEL	CCATCTCG	-	-	rs2776223	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30274437_30274444delCCATCTCG								N6AMT1 (16744 upstream) : RNF160 (26022 downstream)																							tgcaatggcaccatctcgccatctcagc	0.087													9	5	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36337499	36337500	+	Intron	INS	-	CACACACACAGCCT	CACACACACAGCCT	rs146467174	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36337499_36337500insCACACACACAGCCT	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						tcccgcacgtgcacacacacag	0.069			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44467423	44467423	+	IGR	DEL	G	-	-	rs35192629		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44467423delG								PKNOX1 (13735 upstream) : CBS (5878 downstream)																							ctttacataagtggggtcacg	0.000													2	5	---	---	---	---	
PDXK	8566	broad.mit.edu	37	21	45177966	45177966	+	3'UTR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45177966delA	uc002zdm.3	+	11					PDXK_uc010gpj.2_3'UTR|PDXK_uc002zdn.3_3'UTR|PDXK_uc002zdq.3_3'UTR	NM_003681	NP_003672	O00764	PDXK_HUMAN	pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	CCAGCATGAGAACGCAGTGTC	0.483													116	62	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20718476	20718477	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20718476_20718477insA	uc011ahp.1	-	6	775_776	c.476_477insT	c.(475-477)TTGfs	p.L159fs	uc011ahq.1_Frame_Shift_Ins_p.L267fs					SubName: Full=cDNA FLJ59031, highly similar to Ubl carboxyl-terminal hydrolase 18 (EC 3.1.2.-);																		TGTTTCTTACCAAGCAAATATT	0.505													154	77	---	---	---	---	
UPB1	51733	broad.mit.edu	37	22	24919292	24919292	+	Intron	DEL	G	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24919292delG	uc003aaf.2	+						UPB1_uc003aae.2_Intron|UPB1_uc011ajt.1_Intron	NM_016327	NP_057411	Q9UBR1	BUP1_HUMAN	beta-ureidopropionase						pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)					AGCCCCCAGAGTGTGACTTTC	0.562													4	4	---	---	---	---	
UPB1	51733	broad.mit.edu	37	22	24919297	24919298	+	Intron	DEL	AC	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24919297_24919298delAC	uc003aaf.2	+						UPB1_uc003aae.2_Intron|UPB1_uc011ajt.1_Intron	NM_016327	NP_057411	Q9UBR1	BUP1_HUMAN	beta-ureidopropionase						pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)					CCAGAGTGTGACTTTCTGTTTT	0.564													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27858647	27858647	+	IGR	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27858647delT								MIAT (743698 upstream) : MN1 (285619 downstream)																							ctttcttttcttttttttttA	0.383													4	2	---	---	---	---	
CACNA1I	8911	broad.mit.edu	37	22	40052231	40052231	+	Intron	DEL	T	-	-	rs11418217		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40052231delT	uc003ayc.2	+						CACNA1I_uc003ayd.2_Intron|CACNA1I_uc003aye.2_Intron|CACNA1I_uc003ayf.2_Intron	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,						axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)	TGGGTTGTTATTTTTTTTTTC	0.537													3	3	---	---	---	---	
NUP50	10762	broad.mit.edu	37	22	45577378	45577411	+	Intron	DEL	GGAACAGGAAAGAATTCTTGGCCAGTTTATTTAA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45577378_45577411delGGAACAGGAAAGAATTCTTGGCCAGTTTATTTAA	uc003bfr.2	+						NUP50_uc003bfs.2_Intron|NUP50_uc011aqn.1_Intron|NUP50_uc003bft.2_Intron|NUP50_uc011aqo.1_Intron	NM_007172	NP_009103	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa isoform b						carbohydrate metabolic process|glucose transport|intracellular transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore|nucleoplasm	protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GCTCTCAAGTGGAACAGGAAAGAATTCTTGGCCAGTTTATTTAAAAATCCAGTT	0.466													13	6	---	---	---	---	
HDHD1A	8226	broad.mit.edu	37	X	6981319	6981319	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6981319delA	uc004crv.2	-						HDHD1A_uc011mhm.1_Intron|HDHD1A_uc011mhn.1_Intron|HDHD1A_uc010ndl.2_Intron|HDHD1A_uc011mho.1_Intron	NM_012080	NP_036212	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain						nucleotide metabolic process		metal ion binding|phosphatase activity				0		Colorectal(8;0.0114)|Medulloblastoma(8;0.184)				AAAGAATGAGAAAAAATTAAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	7812229	7812229	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7812229delA								VCX (46 upstream) : PNPLA4 (54575 downstream)																							ggagggagggagggaggaaga	0.184													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	7812231	7812233	+	IGR	DEL	GGA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7812231_7812233delGGA								VCX (48 upstream) : PNPLA4 (54571 downstream)																							agggagggagggaggaagaggtg	0.177													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	8310210	8310210	+	IGR	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8310210delC								VCX2 (170902 upstream) : VCX3B (122661 downstream)																							ACTACCTCCACCTCTGTGATT	0.343													4	2	---	---	---	---	
LANCL3	347404	broad.mit.edu	37	X	37511546	37511546	+	Intron	DEL	T	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37511546delT	uc011mkd.1	+						LANCL3_uc004ddp.1_Intron	NM_198511	NP_940913	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3								catalytic activity				0						TTTTATTGACTTTTTTTTTTC	0.284													4	3	---	---	---	---	
PIM2	11040	broad.mit.edu	37	X	48772016	48772016	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48772016delA	uc004dls.2	-						SLC35A2_uc004dlp.1_5'Flank|SLC35A2_uc011mmm.1_5'Flank|SLC35A2_uc011mmn.1_5'Flank	NM_006875	NP_006866	Q9P1W9	PIM2_HUMAN	serine/threonine protein kinase pim-2						anti-apoptosis|cell proliferation|male meiosis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|response to virus		ATP binding|protein serine/threonine kinase activity			lung(3)|stomach(1)	4						TCAACAGAATAAAAGCACTGA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	82254422	82254422	+	IGR	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82254422delA								None (None upstream) : POU3F4 (508847 downstream)																							AGTTTCTCAGAAAAAAAAAAA	0.368													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	86330341	86330343	+	IGR	DEL	TTA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86330341_86330343delTTA								DACH2 (242736 upstream) : KLHL4 (442372 downstream)																							TGTGCATTGCTTATTATTATTAT	0.433													4	2	---	---	---	---	
NXF5	55998	broad.mit.edu	37	X	101097232	101097233	+	Intron	INS	-	T	T			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101097232_101097233insT	uc011mrk.1	-						NXF5_uc004eih.1_Intron|NXF5_uc004eii.1_Intron|NXF5_uc004eij.1_Intron|NXF5_uc004eik.1_Intron|NXF5_uc004eil.1_Intron	NM_032946	NP_116564	Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5						mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nucleus	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1						ttctttctttcttccatttctt	0.149													4	4	---	---	---	---	
NXF5	55998	broad.mit.edu	37	X	101097235	101097236	+	Intron	INS	-	TTT	TTT	rs5986863	by1000genomes	TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101097235_101097236insTTT	uc011mrk.1	-						NXF5_uc004eih.1_Intron|NXF5_uc004eii.1_Intron|NXF5_uc004eij.1_Intron|NXF5_uc004eik.1_Intron|NXF5_uc004eil.1_Intron	NM_032946	NP_116564	Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5						mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nucleus	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1						tttctttcttccatttctttct	0.144													3	4	---	---	---	---	
NRK	203447	broad.mit.edu	37	X	105197382	105197382	+	Intron	DEL	A	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105197382delA	uc004emd.2	+						NRK_uc011msi.1_Intron	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase								ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14						GCTCATTTTGAAAAAAATAAG	0.269										HNSCC(51;0.14)			4	2	---	---	---	---	
WDR44	54521	broad.mit.edu	37	X	117519652	117519653	+	Intron	INS	-	G	G			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117519652_117519653insG	uc004eqn.2	+						WDR44_uc004eqo.2_Intron|WDR44_uc011mtr.1_Intron|MIR1277_hsa-mir-1277|MI0006419_5'Flank	NM_019045	NP_061918	Q5JSH3	WDR44_HUMAN	WD repeat domain 44 protein							cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5						ataatgtgatagaaagttaagg	0.050													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	121573258	121573259	+	IGR	INS	-	A	A	rs146412714		TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:121573258_121573259insA								None (None upstream) : GRIA3 (744837 downstream)																							atggaggaggcagcagggaggt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	129261012	129261013	+	IGR	DEL	GT	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129261012_129261013delGT								ELF4 (16324 upstream) : AIFM1 (2327 downstream)																							aataaaccaggtgtgtgtgtgt	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	142643638	142643639	+	IGR	DEL	GA	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142643638_142643639delGA								SPANXN3 (38331 upstream) : SLITRK4 (72306 downstream)																							atcttccctggacctccTCCCT	0.173													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	152373219	152373219	+	IGR	DEL	C	-	-			TCGA-CJ-4634-01A-02D-1386-10	TCGA-CJ-4634-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152373219delC								PNMA6A (129818 upstream) : MAGEA1 (108303 downstream)																							ACCTGCACCTCCCCCCCCCAA	0.398													7	6	---	---	---	---	
