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	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
MMP3	4314	broad.mit.edu	36	11	102215173	102215173	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:102215173C>T	uc001phj.1	-	c.947G>A	c.(946-948)CGC>CAC	p.R316H		NM_002422	NP_002413	P08254	MMP3_HUMAN	matrix metalloproteinase 3 preproprotein	316	Hemopexin-like 1.				collagen catabolic process|proteolysis	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			lung(1)|kidney(1)	2		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)			Marimastat(DB00786)|Simvastatin(DB00641)									0.272727	84.023373	89.656101	33	88	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Missense_Mutation	SNP	102215173	102215173	10057	11	C	T	T	27	27	MMP3	T	1	1
TRIM29	23650	broad.mit.edu	36	11	119513481	119513481	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:119513481C>T	uc001pwz.1	-	c.469G>A	c.(469-471)GAC>AAC	p.D157N	TRIM29_uc001pxa.1_Non-coding_Transcript	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29	157					transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)|kidney(1)	3		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)												0.433155	225.53195	226.259661	81	106	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)	Missense_Mutation	SNP	119513481	119513481	17047	11	C	T	T	31	31	TRIM29	T	1	1
P2RX3	5024	broad.mit.edu	36	11	56862645	56862645	+	Silent	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56862645G>A	uc001nju.1	+	c.45G>A	c.(43-45)TCG>TCA	p.S15S	SSRP1_uc001njt.1_5'Flank	NM_002559	NP_002550	P56373	P2RX3_HUMAN	purinergic receptor P2X3	15	Cytoplasmic (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0														0.398844	418.034353	421.112643	138	208	GG		KEEP	---	---	---	---	capture			Silent	SNP	56862645	56862645	11754	11	G	A	A	39	39	P2RX3	A	1	1
FOLR4	390243	broad.mit.edu	36	11	93680020	93680020	+	Silent	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:93680020G>A	uc001pes.1	+	c.369G>A	c.(367-369)CCG>CCA	p.P123P		NM_001080486	NP_001073955	A6ND01	FOLR4_HUMAN	folate receptor 4 (delta) homolog	130						extracellular region	folic acid binding|receptor activity			ovary(1)	1														0.423077	29.718803	29.853325	11	15	GG		KEEP	---	---	---	---	capture			Silent	SNP	93680020	93680020	6226	11	G	A	A	38	38	FOLR4	A	1	1
GLT8D2	83468	broad.mit.edu	36	12	102914710	102914710	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:102914710G>A	uc001tkh.1	-	c.533C>T	c.(532-534)GCG>GTG	p.A178V	GLT8D2_uc001tki.1_Missense_Mutation_p.A178V	NM_031302	NP_112592	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	178	Lumenal (Potential).					integral to membrane	transferase activity, transferring glycosyl groups			ovary(1)	1														0.4	178.29534	179.684991	64	96	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102914710	102914710	6738	12	G	A	A	38	38	GLT8D2	A	1	1
MMP17	4326	broad.mit.edu	36	12	130888711	130888711	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:130888711G>A	uc001ujc.1	+	c.178G>A	c.(178-180)GGT>AGT	p.G60S	MMP17_uc001ujd.1_5'UTR	NM_016155	NP_057239	Q9ULZ9	MMP17_HUMAN	matrix metalloproteinase 17 preproprotein	60					proteolysis	anchored to membrane|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)													0.396226	64.263496	64.763119	21	32	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Missense_Mutation	SNP	130888711	130888711	10046	12	G	A	A	39	39	MMP17	A	1	1
IQSEC3	440073	broad.mit.edu	36	12	145185	145185	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:145185C>A	uc001qhw.1	+	c.1930C>A	c.(1930-1932)CCG>ACG	p.P644T	IQSEC3_uc001qhu.1_Missense_Mutation_p.P644T	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	947	PH.				regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity	p.P644T(1)		central_nervous_system(2)|large_intestine(1)	3	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)													0.404762	94.425159	95.093031	34	50	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)	Missense_Mutation	SNP	145185	145185	8122	12	C	A	A	22	22	IQSEC3	A	3	3
CYP27B1	1594	broad.mit.edu	36	12	56445097	56445097	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56445097G>A	uc001spz.1	-	c.754C>T	c.(754-756)CGC>TGC	p.R252C	CYP27B1_uc001sqa.1_Missense_Mutation_p.R17C|CYP27B1_uc001sqb.1_Missense_Mutation_p.P132L|CYP27B1_uc001sqc.1_Missense_Mutation_p.P132L	NM_000785	NP_000776	O15528	CP27B_HUMAN	cytochrome P450, family 27, subfamily B,	252					bone mineralization|calcium ion homeostasis|calcium ion transport|decidualization|G1 to G0 transition|hormone biosynthetic process|negative regulation of calcidiol 1-monooxygenase activity|negative regulation of cell growth|negative regulation of cell proliferation|oxidation-reduction process|positive regulation of keratinocyte differentiation|positive regulation of vitamin D 24-hydroxylase activity|positive regulation of vitamin D receptor signaling pathway|regulation of bone mineralization|response to estrogen stimulus|response to interferon-gamma|response to lipopolysaccharide|response to tumor necrosis factor|response to vitamin D|vitamin D biosynthetic process|xenobiotic metabolic process	mitochondrial outer membrane	calcidiol 1-monooxygenase activity|electron carrier activity|heme binding	p.R252C(1)		central_nervous_system(3)	3	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)				Calcidiol(DB00146)|Calcitriol(DB00136)|Ergocalciferol(DB00153)					101		OREG0021953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.403846	124.150724	124.984381	42	62	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		Missense_Mutation	SNP	56445097	56445097	4324	12	G	A	A	39	39	CYP27B1	A	1	1
TMTC4	84899	broad.mit.edu	36	13	100113358	100113358	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:100113358G>A	uc001vot.1	-	c.413C>T	c.(412-414)TCT>TTT	p.S138F	TMTC4_uc001vou.1_Missense_Mutation_p.S119F	NM_032813	NP_001073137	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat	119	Helical; (Potential).					integral to membrane	binding			ovary(2)|breast(1)	3	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)													0.346405	153.885973	157.092168	53	100	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100113358	100113358	16804	13	G	A	A	33	33	TMTC4	A	2	2
DACT1	51339	broad.mit.edu	36	14	58183129	58183129	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0211-01	TCGA-06-0211-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:58183129T>G	uc001xdw.1	+	c.2035T>G	c.(2035-2037)TGG>GGG	p.W679G	DACT1_uc001xdx.1_Missense_Mutation_p.W642G	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1	679					multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5														0.384615	6.808821	6.979868	5	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58183129	58183129	4388	14	T	G	G	59	59	DACT1	G	4	4
SYT16	83851	broad.mit.edu	36	14	61617548	61617548	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:61617548G>A	uc001xfu.1	+	c.1237G>A	c.(1237-1239)GTC>ATC	p.V413I		NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	413	C2 1.									central_nervous_system(1)	1														0.446809	62.469078	62.584878	21	26	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)	Missense_Mutation	SNP	61617548	61617548	15993	14	G	A	A	40	40	SYT16	A	1	1
CKMT1A	548596	broad.mit.edu	36	15	41778521	41778521	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41778521G>A	uc001zsn.1	+	c.1196G>A	c.(1195-1197)CGT>CAT	p.R399H	CKMT1A_uc001zso.2_Missense_Mutation_p.R399H	NM_001015001	NP_066270	P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1A precursor	399	Phosphagen kinase C-terminal.				creatine metabolic process	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)			Creatine(DB00148)									0.462963	286.665529	286.924367	100	116	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(94;3.56e-07)	Missense_Mutation	SNP	41778521	41778521	3585	15	G	A	A	40	40	CKMT1A	A	1	1
TMOD3	29766	broad.mit.edu	36	15	49942416	49942416	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:49942416C>A	uc002abm.1	+	c.43C>A	c.(43-45)CTT>ATT	p.L15I		NM_014547	NP_055362	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	15						cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1						Colon(122;1837 2251 18387 22826)								0.456376	200.772399	201.020441	68	81	CC		KEEP	---	---	---	---	capture		all cancers(107;0.00194)	Missense_Mutation	SNP	49942416	49942416	16775	15	C	A	A	24	24	TMOD3	A	3	3
ACAN	176	broad.mit.edu	36	15	87203231	87203231	+	Silent	SNP	C	T	T	rs34543273	by-1000genomes	TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:87203231C>T	uc002bmy.1	+	c.6069C>T	c.(6067-6069)CAC>CAT	p.H2023H	ACAN_uc002bmz.1_Silent_p.H2023H|ACAN_uc002bna.1_Silent_p.H267H	NM_013227	NP_037359			aggrecan isoform 2 precursor											ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)													0.442308	202.152837	202.604924	69	87	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.146)		Silent	SNP	87203231	87203231	118	15	C	T	T	19	19	ACAN	T	1	1
MYOCD	93649	broad.mit.edu	36	17	12590049	12590049	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0211-01	TCGA-06-0211-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:12590049T>G	uc002gno.1	+	c.1060T>G	c.(1060-1062)TCT>GCT	p.S354A	MYOCD_uc002gnn.1_Missense_Mutation_p.S354A|MYOCD_uc002gnp.1_Missense_Mutation_p.S258A|MYOCD_uc002gnq.1_Missense_Mutation_p.S73A	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin	354					cardiac cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of smooth muscle contraction|regulation of smooth muscle cell differentiation|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription factor binding			central_nervous_system(2)|ovary(1)	3														0.480836	499.550182	499.641191	138	149	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)	Missense_Mutation	SNP	12590049	12590049	10482	17	T	G	G	62	62	MYOCD	G	4	4
NCOR1	9611	broad.mit.edu	36	17	15908176	15908176	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:15908176G>A	uc002gpo.1	-	c.5152C>T	c.(5152-5154)CGG>TGG	p.R1718W	NCOR1_uc002gpn.1_Missense_Mutation_p.R1734W|NCOR1_uc002gpm.1_Missense_Mutation_p.R238W|NCOR1_uc010coy.1_Missense_Mutation_p.R626W	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1	1718	Interaction with ETO.|Interaction with C1D (By similarity).				cellular lipid metabolic process|chromatin modification|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of JNK cascade|regulation of fatty acid transport|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	spindle microtubule|transcriptional repressor complex	histone deacetylase binding|promoter binding|transcription corepressor activity			ovary(1)|kidney(1)	2														0.414062	149.86267	150.684561	53	75	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)	Missense_Mutation	SNP	15908176	15908176	10634	17	G	A	A	40	40	NCOR1	A	1	1
ABI3	51225	broad.mit.edu	36	17	44652599	44652599	+	Silent	SNP	C	A	A			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:44652599C>A	uc002iop.1	+	c.714C>A	c.(712-714)CCC>CCA	p.P238P	ABI3_uc002ioq.1_Silent_p.P232P	NM_016428	NP_057512	Q9P2A4	ABI3_HUMAN	NESH protein isoform 1	238	Pro-rich.				cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0														0.464286	37.971177	38.002374	13	15	CC		KEEP	---	---	---	---	capture	Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)		Silent	SNP	44652599	44652599	91	17	C	A	A	21	21	ABI3	A	3	3
SETBP1	26040	broad.mit.edu	36	18	40784933	40784933	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:40784933C>T	uc010dni.1	+	c.1468C>T	c.(1468-1470)CGA>TGA	p.R490*	SETBP1_uc002laz.1_Nonsense_Mutation_p.R490*	NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	544						nucleus	DNA binding			large_intestine(1)	1														0.365922	369.847271	375.498944	131	227	CC		KEEP	---	---	---	---	capture		Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)	Nonsense_Mutation	SNP	40784933	40784933	14617	18	C	T	T	31	31	SETBP1	T	5	1
KDSR	2531	broad.mit.edu	36	18	59185315	59185315	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59185315G>C	uc010dpw.1	-	c.17C>G	c.(16-18)GCC>GGC	p.A6G		NM_002035	NP_002026	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase precursor	6					3-keto-sphinganine metabolic process|oxidation-reduction process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding				0									p.A6G(SNU719-Tumor)	107				0.266667	8.003985	8.735529	4	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59185315	59185315	8446	18	G	C	C	42	42	KDSR	C	3	3
PODNL1	79883	broad.mit.edu	36	19	13907600	13907600	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:13907600G>A	uc002mxr.1	-	c.449C>T	c.(448-450)GCG>GTG	p.A150V	PODNL1_uc002mxs.1_Intron	NM_024825	NP_079101	Q6PEZ8	PONL1_HUMAN	podocan-like 1	150	Leu-rich.|LRR 4.					proteinaceous extracellular matrix				central_nervous_system(1)	1														0.350877	54.092004	55.205926	20	37	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)		Missense_Mutation	SNP	13907600	13907600	12607	19	G	A	A	38	38	PODNL1	A	1	1
ZNF254	9534	broad.mit.edu	36	19	24102570	24102570	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:24102570C>G	uc002nru.1	+	c.1928C>G	c.(1927-1929)TCG>TGG	p.S643W		NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254	643					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)												0.242105	210.56873	227.82794	69	216	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24102570	24102570	18389	19	C	G	G	31	31	ZNF254	G	3	3
CIC	23152	broad.mit.edu	36	19	47489093	47489093	+	Silent	SNP	G	C	C			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47489093G>C	uc002otf.1	+	c.3615G>C	c.(3613-3615)CGG>CGC	p.R1205R		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	1205	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)	8		Prostate(69;0.00682)								241				0.315789	7.528139	8.172523	6	13	GG		KEEP	---	---	---	---	capture			Silent	SNP	47489093	47489093	3558	19	G	C	C	42	42	CIC	C	3	3
FKRP	79147	broad.mit.edu	36	19	51951575	51951575	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0211-01	TCGA-06-0211-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:51951575A>C	uc002pfn.1	+	c.1028A>C	c.(1027-1029)GAG>GCG	p.E343A	FKRP_uc002pfo.1_Missense_Mutation_p.E343A|FKRP_uc002pfp.1_Missense_Mutation_p.E343A|FKRP_uc010eku.1_Missense_Mutation_p.E343A	NM_024301	NP_077277	Q9H9S5	FKRP_HUMAN	fukutin-related protein	343						extracellular space|Golgi apparatus|rough endoplasmic reticulum|sarcolemma	transferase activity			pancreas(1)	1		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)												0.375	8.024604	8.133688	3	5	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)	Missense_Mutation	SNP	51951575	51951575	6155	19	A	C	C	11	11	FKRP	C	4	4
SIGLEC10	89790	broad.mit.edu	36	19	56610993	56610993	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0211-01	TCGA-06-0211-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56610993T>C	uc002pwo.1	-	c.995A>G	c.(994-996)CAG>CGG	p.Q332R	SIGLEC10_uc002pwp.1_Missense_Mutation_p.Q274R|SIGLEC10_uc002pwq.1_Missense_Mutation_p.Q274R|SIGLEC10_uc002pwr.1_Missense_Mutation_p.Q332R|SIGLEC10_uc010eow.1_Missense_Mutation_p.Q144R|SIGLEC10_uc002pws.1_Intron	NM_033130	NP_149121	Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	332	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion	extracellular region|integral to membrane|plasma membrane	sugar binding				0		all_neural(266;0.0199)												0.21371	85.823884	105.054527	53	195	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)	Missense_Mutation	SNP	56610993	56610993	14801	19	T	C	C	55	55	SIGLEC10	C	4	4
LILRB5	10990	broad.mit.edu	36	19	59451752	59451752	+	Silent	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59451752C>T	uc002qey.1	-	c.621G>A	c.(619-621)TCG>TCA	p.S207S	LILRA6_uc002qew.1_Intron|LILRB5_uc002qex.1_Silent_p.S207S|LILRB5_uc002qez.1_Intron|LILRB5_uc002qfa.1_Intron	NM_001081442	NP_001074911	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,	207	Extracellular (Potential).|Ig-like C2-type 2.				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)													0.269841	128.420427	137.471021	51	138	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.105)	Silent	SNP	59451752	59451752	9120	19	C	T	T	31	31	LILRB5	T	1	1
KIR2DL4	3805	broad.mit.edu	36	19	60017138	60017138	+	Silent	SNP	G	T	T			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60017138G>T	uc002qhc.1	+	c.954G>T	c.(952-954)GTG>GTT	p.V318V	KIR2DS4_uc010erv.1_Intron|KIR2DS4_uc010erx.1_Intron|KIR2DS4_uc010esa.1_Intron|KIR3DL1_uc002qhd.2_Intron|KIR3DL1_uc010esb.1_Intron|KIR3DL1_uc010esf.1_5'Flank|KIR3DL1_uc002qhk.2_5'Flank|KIR3DL1_uc002qhl.2_5'Flank|KIR2DL4_uc010esc.1_3'UTR|KIR2DL4_uc002qhi.1_3'UTR|KIR2DL4_uc002qhh.1_Silent_p.V168V|KIR2DL4_uc002qhj.1_Silent_p.V246V|KIR2DL4_uc010esd.1_3'UTR|KIR2DL4_uc002qhf.1_Silent_p.V151V|KIR2DL4_uc002qhg.1_Silent_p.V263V|KIR2DL4_uc010ese.1_Non-coding_Transcript	NM_002255	NP_002246	Q99706	KI2L4_HUMAN	killer cell immunoglobulin-like receptor, two	298	Cytoplasmic (Potential).		Missing (in allele KIR2DL4*0501).		cellular defense response|regulation of immune response	integral to plasma membrane	protein binding|transmembrane receptor activity			ovary(1)	1														0.282723	131.053922	139.164801	54	137	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0192)	Silent	SNP	60017138	60017138	8630	19	G	T	T	45	45	KIR2DL4	T	3	3
NLRP13	126204	broad.mit.edu	36	19	61116382	61116382	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61116382G>A	uc002qmg.1	-	c.613C>T	c.(613-615)CGT>TGT	p.R205C		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	205							ATP binding			ovary(3)|skin(2)|pancreas(1)|lung(1)	7		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)												0.242171	293.785799	322.808347	116	363	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0642)	Missense_Mutation	SNP	61116382	61116382	10878	19	G	A	A	39	39	NLRP13	A	1	1
MUC16	94025	broad.mit.edu	36	19	8837821	8837821	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8837821G>A	uc002mkp.1	-	c.42245C>T	c.(42244-42246)ACC>ATC	p.T14082I	MUC16_uc010dwh.1_Intron|MUC16_uc010dwi.1_Non-coding_Transcript|MUC16_uc010dwj.1_Missense_Mutation_p.T882I	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	14112	SEA 14.|Extracellular (Potential).			Missing (in Ref. 3; AAK74120).	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.27451	69.438915	74.124059	28	74	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8837821	8837821	10367	19	G	A	A	44	44	MUC16	A	2	2
FAM63A	55793	broad.mit.edu	36	1	149241619	149241619	+	Silent	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:149241619C>T	uc001ewb.1	-	c.99G>A	c.(97-99)GAG>GAA	p.E33E	FAM63A_uc001ewc.1_Intron|FAM63A_uc001ewd.1_Intron|FAM63A_uc001ewe.1_Intron|FAM63A_uc001ewf.1_Silent_p.E33E|FAM63A_uc001ewg.1_Silent_p.E33E	NM_018379	NP_060849	Q8N5J2	FA63A_HUMAN	hypothetical protein LOC55793 isoform 1	33							protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)													0.225806	209.929939	237.7697	91	312	CC		KEEP	---	---	---	---	capture	UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)		Silent	SNP	149241619	149241619	5819	1	C	T	T	28	28	FAM63A	T	2	2
FLG	2312	broad.mit.edu	36	1	150551097	150551097	+	Silent	SNP	A	G	G			TCGA-06-0211-01	TCGA-06-0211-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150551097A>G	uc001ezu.1	-	c.2889T>C	c.(2887-2889)TCT>TCC	p.S963S		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	963	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.453448	814.617188	815.715125	263	317	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Silent	SNP	150551097	150551097	6160	1	A	G	G	7	7	FLG	G	4	4
DPT	1805	broad.mit.edu	36	1	166964798	166964798	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:166964798G>A	uc001gfp.1	-	c.239C>T	c.(238-240)ACG>ATG	p.T80M		NM_001937	NP_001928	Q07507	DERM_HUMAN	dermatopontin precursor	80	2 X 53-55 AA tandem repeats.|1-2.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion	extracellular space|proteinaceous extracellular matrix				ovary(1)	1	all_hematologic(923;0.208)													0.457143	324.823582	325.219976	112	133	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166964798	166964798	4923	1	G	A	A	40	40	DPT	A	1	1
YOD1	55432	broad.mit.edu	36	1	205289523	205289523	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:205289523C>T	uc001hfe.1	-	c.512G>A	c.(511-513)GGA>GAA	p.G171E	YOD1_uc001hff.1_Missense_Mutation_p.G127E	NM_018566	NP_061036	Q5VVQ6	OTU1_HUMAN	YOD1 OTU deubiquinating enzyme 1 homolog	171	OTU.				cellular amino acid metabolic process|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination	intracellular	protein binding|ubiquitin-specific protease activity|zinc ion binding				0	Prostate(682;0.19)													0.43299	125.633609	126.013742	42	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	205289523	205289523	18071	1	C	T	T	30	30	YOD1	T	2	2
LDLRAD2	401944	broad.mit.edu	36	1	22015026	22015026	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:22015026C>T	uc001bfg.1	+	c.515C>T	c.(514-516)CCT>CTT	p.P172L		NM_001013693	NP_001013715	Q5SZI1	LRAD2_HUMAN	low density lipoprotein receptor class A domain	172	Extracellular (Potential).|LDL-receptor class A.					integral to membrane	receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.00166)|all_lung(284;0.00172)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)												0.391667	141.770056	143.011298	47	73	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;5.2e-26)|COAD - Colon adenocarcinoma(152;1.13e-05)|GBM - Glioblastoma multiforme(114;1.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00598)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)	Missense_Mutation	SNP	22015026	22015026	9030	1	C	T	T	24	24	LDLRAD2	T	2	2
ITSN1	6453	broad.mit.edu	36	21	34096618	34096618	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:34096618G>A	uc002yta.1	+	c.2319G>A	c.(2317-2319)TGG>TGA	p.W773*	DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.2_Intron|ITSN1_uc002ysz.1_Intron|ITSN1_uc010gmg.1_Intron|ITSN1_uc010gmh.1_Intron|ITSN1_uc002ysw.1_Nonsense_Mutation_p.W773*|ITSN1_uc010gmi.1_Nonsense_Mutation_p.W736*|ITSN1_uc010gmj.1_Intron|ITSN1_uc002ysy.1_Intron|ITSN1_uc002ysx.1_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytc.1_Intron|ITSN1_uc002ytd.1_Intron|ITSN1_uc010gmk.1_Nonsense_Mutation_p.W736*|ITSN1_uc010gml.1_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc002yte.1_Nonsense_Mutation_p.W707*|ITSN1_uc002ytf.1_Non-coding_Transcript	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l	773	SH3 1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)	3														0.387097	447.449079	451.591497	144	228	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	34096618	34096618	8230	21	G	A	A	43	43	ITSN1	A	5	2
C22orf36	388886	broad.mit.edu	36	22	23311925	23311925	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0211-01	TCGA-06-0211-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:23311925T>G	uc003aaq.2	-	c.877A>C	c.(877-879)ACC>CCC	p.T293P	GGT1_uc003aan.1_Intron|C22orf36_uc003aao.2_Non-coding_Transcript|C22orf36_uc003aap.2_Non-coding_Transcript	NM_207644	NP_997527	Q2VPJ9	LRC6X_HUMAN	hypothetical protein LOC388886	293											0														0.290323	7.195354	8.614294	9	22	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23311925	23311925	2227	22	T	G	G	59	59	C22orf36	G	4	4
PLXNB2	23654	broad.mit.edu	36	22	49063290	49063290	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49063290G>C	uc003bkv.2	-	c.2964C>G	c.(2962-2964)TTC>TTG	p.F988L	PLXNB2_uc003bkt.1_5'Flank|PLXNB2_uc003bku.1_5'Flank	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2	988	IPT/TIG 3.|Extracellular (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)	5		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.272727	7.220267	7.732384	3	8	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49063290	49063290	12550	22	G	C	C	37	37	PLXNB2	C	3	3
DPP10	57628	broad.mit.edu	36	2	116289736	116289736	+	Silent	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:116289736G>A	uc002tla.1	+	c.1911G>A	c.(1909-1911)CTG>CTA	p.L637L	DPP10_uc002tlb.1_Silent_p.L587L|DPP10_uc002tlc.1_Silent_p.L633L|DPP10_uc002tle.1_Silent_p.L587L|DPP10_uc002tlf.1_Silent_p.L630L	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	637	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|breast(1)|skin(1)	9														0.481481	75.84354	75.85984	26	28	GG		KEEP	---	---	---	---	capture			Silent	SNP	116289736	116289736	4911	2	G	A	A	46	46	DPP10	A	2	2
RAD51AP2	729475	broad.mit.edu	36	2	17562523	17562523	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:17562523G>T	uc002rcl.1	-	c.641C>A	c.(640-642)GCT>GAT	p.A214D	RAD51AP2_uc010exn.1_Missense_Mutation_p.A205D	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	214										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)													0.34127	118.880211	121.688774	43	83	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17562523	17562523	13447	2	G	T	T	34	34	RAD51AP2	T	3	3
UGT1A1	54658	broad.mit.edu	36	2	234333697	234333697	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234333697C>T	uc002vvb.1	+	c.25C>T	c.(25-27)CGC>TGC	p.R9C	UGT1A8_uc002vup.1_Intron|UGT1A10_uc002vuq.2_Intron|UGT1A10_uc002vur.1_Intron|UGT1A9_uc002vus.1_Intron|UGT1A7_uc002vut.1_Intron|UGT1A6_uc002vuu.1_Intron|UGT1A6_uc002vuv.2_Intron|UGT1A5_uc002vuw.1_Intron|UGT1A4_uc002vux.1_Intron|UGT1A3_uc002vuy.1_Intron|UGT1A10_uc002vva.1_Intron	NM_000463	NP_000454	P22309	UD11_HUMAN	UDP glycosyltransferase 1 family, polypeptide A1	9					bilirubin conjugation|digestion|drug metabolic process|estrogen metabolic process|flavone metabolic process|heme catabolic process|negative regulation of steroid metabolic process|retinoic acid metabolic process	endoplasmic reticulum membrane|microsome	enzyme binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding|steroid binding			central_nervous_system(1)	1		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)			Abacavir(DB01048)|Adenine(DB00173)|Diclofenac(DB00586)|Estradiol(DB00783)|Ezetimibe(DB00973)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Rifampin(DB01045)|Troglitazone(DB00197)							OREG0003837	type=REGULATORY REGION|Gene=UGT1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.418182	63.733248	64.049382	23	32	CC		KEEP	---	---	---	---	capture		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Missense_Mutation	SNP	234333697	234333697	17502	2	C	T	T	19	19	UGT1A1	T	1	1
SETD2	29072	broad.mit.edu	36	3	47033658	47033658	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:47033658C>T	uc003cqs.1	-	c.6115G>A	c.(6115-6117)GAG>AAG	p.E2039K	SETD2_uc003cqr.1_Missense_Mutation_p.E141K	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2542	Interaction with POLR2A.				oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)												0.513699	234.528293	234.552293	75	71	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)	Missense_Mutation	SNP	47033658	47033658	14620	3	C	T	T	30	30	SETD2	T	2	2
ADH7	131	broad.mit.edu	36	4	100568301	100568301	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:100568301G>A	uc003huv.1	-	c.349C>T	c.(349-351)CGC>TGC	p.R117C		NM_000673	NP_000664	P40394	ADH7_HUMAN	alcohol dehydrogenase 7	117					ethanol oxidation|fatty acid omega-oxidation|response to bacterium|response to ethanol|xenobiotic metabolic process	cytosol|soluble fraction	alcohol dehydrogenase activity, zinc-dependent|aldehyde oxidase activity|ethanol binding|receptor antagonist activity|retinol binding|retinol dehydrogenase activity			lung(2)	2					NADH(DB00157)									0.450495	275.100136	275.531386	91	111	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)	Missense_Mutation	SNP	100568301	100568301	314	4	G	A	A	37	37	ADH7	A	1	1
UGT2B4	7363	broad.mit.edu	36	4	70395635	70395635	+	Silent	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70395635G>A	uc003hek.2	-	c.534C>T	c.(532-534)TAC>TAT	p.Y178Y	UGT2B4_uc003hel.2_Silent_p.Y178Y	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family,	178					estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0														0.452381	164.657277	164.906322	57	69	GG		KEEP	---	---	---	---	capture			Silent	SNP	70395635	70395635	17519	4	G	A	A	40	40	UGT2B4	A	1	1
FAM190A	401145	broad.mit.edu	36	4	91608467	91608467	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0211-01	TCGA-06-0211-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:91608467A>G	uc003hsv.2	+	c.1663A>G	c.(1663-1665)ATG>GTG	p.M555V	FAM190A_uc010ikv.1_Non-coding_Transcript|FAM190A_uc003hsw.1_Missense_Mutation_p.M555V	NM_207491	NP_997374	Q9C0I3	F190A_HUMAN	similar to KIAA1680 protein isoform 2	555										large_intestine(1)|ovary(1)	2														0.409091	62.843598	63.160796	18	26	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	91608467	91608467	5732	4	A	G	G	16	16	FAM190A	G	4	4
PCDHGB3	56102	broad.mit.edu	36	5	140731241	140731241	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140731241G>A	uc003ljw.1	+	c.1096G>A	c.(1096-1098)GTT>ATT	p.V366I	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGA6_uc003ljy.1_5'Flank|PCDHGB3_uc003ljv.1_Missense_Mutation_p.V366I|PCDHGA6_uc003ljx.1_5'Flank	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	366	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.459459	50.33314	50.377273	17	20	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140731241	140731241	11984	5	G	A	A	40	40	PCDHGB3	A	1	1
SLIT3	6586	broad.mit.edu	36	5	168113490	168113490	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:168113490C>T	uc010jjg.1	-	c.1786G>A	c.(1786-1788)GTG>ATG	p.V596M	SLIT3_uc003mab.1_Missense_Mutation_p.V596M	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3	596	LRR 14.				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)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)				Ovarian(29;311 847 10864 17279 24903)								0.444444	81.895206	82.063754	28	35	CC		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	168113490	168113490	15239	5	C	T	T	19	19	SLIT3	T	1	1
GRM6	2916	broad.mit.edu	36	5	178346474	178346474	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:178346474C>G	uc003mjr.1	-	c.1471G>C	c.(1471-1473)GGC>CGC	p.G491R	GRM6_uc003mjq.1_5'Flank|GRM6_uc010jla.1_Missense_Mutation_p.G74R|GRM6_uc003mjs.1_Missense_Mutation_p.G111R	NM_000843	NP_000834	O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6 precursor	491	Extracellular (Potential).				detection of visible light|visual perception	integral to plasma membrane				ovary(2)|breast(1)|pancreas(1)	4	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)												0.512821	57.895143	57.897725	20	19	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)	Missense_Mutation	SNP	178346474	178346474	7080	5	C	G	G	22	22	GRM6	G	3	3
CARD6	84674	broad.mit.edu	36	5	40888338	40888338	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0211-01	TCGA-06-0211-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:40888338A>G	uc003jmg.1	+	c.1147A>G	c.(1147-1149)ATG>GTG	p.M383V		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	383					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5														0.337209	88.660575	90.670485	29	57	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40888338	40888338	2769	5	A	G	G	8	8	CARD6	G	4	4
HEATR7B2	133558	broad.mit.edu	36	5	41097503	41097503	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41097503G>A	uc003jmj.2	-	c.541C>T	c.(541-543)CGA>TGA	p.R181*		NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	181							binding			ovary(6)|central_nervous_system(2)	8														0.442029	371.780825	372.5923	122	154	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	41097503	41097503	7318	5	G	A	A	39	39	HEATR7B2	A	5	1
HCN1	348980	broad.mit.edu	36	5	45303108	45303108	+	Silent	SNP	A	T	T			TCGA-06-0211-01	TCGA-06-0211-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:45303108A>T	uc003jok.1	-	c.1623T>A	c.(1621-1623)ATT>ATA	p.I541I		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	541	cAMP.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.418605	149.299454	150.050953	54	75	AA		KEEP	---	---	---	---	capture			Silent	SNP	45303108	45303108	7278	5	A	T	T	1	1	HCN1	T	4	4
OR14J1	442191	broad.mit.edu	36	6	29382590	29382590	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29382590G>A	uc003nmc.1	+	c.145G>A	c.(145-147)GTG>ATG	p.V49M		NM_030946	NP_112208	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 5, subfamily U member	49	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.389831	260.648598	263.156611	92	144	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29382590	29382590	11354	6	G	A	A	40	40	OR14J1	A	1	1
CLIC5	53405	broad.mit.edu	36	6	46025060	46025060	+	Silent	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:46025060C>T	uc003oxv.2	-	c.687G>A	c.(685-687)ACG>ACA	p.T229T	CLIC5_uc003oxu.2_Silent_p.T70T|CLIC5_uc003oxx.2_Silent_p.T70T	NM_001114086	NP_001107558	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5 isoform a	229					female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity			ovary(1)	1														0.436681	279.147473	279.950409	100	129	CC		KEEP	---	---	---	---	capture			Silent	SNP	46025060	46025060	3667	6	C	T	T	27	27	CLIC5	T	1	1
COL19A1	1310	broad.mit.edu	36	6	70699420	70699420	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0211-01	TCGA-06-0211-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:70699420T>A	uc003pfc.1	+	c.691T>A	c.(691-693)TAC>AAC	p.Y231N	COL19A1_uc010kam.1_Missense_Mutation_p.Y127N	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	231	TSP N-terminal.				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4														0.375	51.437074	52.095888	18	30	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70699420	70699420	3814	6	T	A	A	53	53	COL19A1	A	4	4
KCNQ5	56479	broad.mit.edu	36	6	73961396	73961396	+	Silent	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:73961396C>T	uc003pgk.1	+	c.2337C>T	c.(2335-2337)GAC>GAT	p.D779D	KCNQ5_uc010kat.1_Silent_p.D770D	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	779					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)	6		all_epithelial(107;0.116)|Lung NSC(302;0.219)				GBM(142;1375 1859 14391 23261 44706)								0.423913	112.911741	113.375723	39	53	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Silent	SNP	73961396	73961396	8391	6	C	T	T	19	19	KCNQ5	T	1	1
REPIN1	29803	broad.mit.edu	36	7	149700592	149700592	+	Silent	SNP	C	A	A			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149700592C>A	uc010lpr.1	+	c.1500C>A	c.(1498-1500)GGC>GGA	p.G500G	REPIN1_uc003whd.2_Silent_p.G432G|REPIN1_uc010lpq.1_Silent_p.G443G|REPIN1_uc003whc.2_Silent_p.G443G|REPIN1_uc003whe.2_Silent_p.G443G	NM_001099695	NP_001093165	Q9BWE0	REPI1_HUMAN	replication initiator 1 isoform 3	443	C2H2-type 11.				DNA replication	nuclear origin of replication recognition complex	DNA binding|zinc ion binding			pancreas(1)	1	Ovarian(565;0.183)|Melanoma(164;0.226)													0.304348	18.815671	19.601616	7	16	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.011)		Silent	SNP	149700592	149700592	13696	7	C	A	A	25	25	REPIN1	A	3	3
HDAC9	9734	broad.mit.edu	36	7	18835332	18835332	+	Silent	SNP	C	A	A			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:18835332C>A	uc003sui.1	+	c.2346C>A	c.(2344-2346)CCC>CCA	p.P782P	HDAC9_uc003sue.1_Silent_p.P779P|HDAC9_uc003suh.1_Silent_p.P779P|HDAC9_uc003suj.1_Silent_p.P738P|HDAC9_uc003suk.1_Silent_p.P27P|HDAC9_uc003sua.1_Silent_p.P757P|HDAC9_uc003sug.1_Silent_p.P779P	NM_178425	NP_848512	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 5	779	Histone deacetylase.				B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|specific transcriptional repressor activity|transcription corepressor activity|transcription repressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)									0.265873	161.536811	174.005034	67	185	CC		KEEP	---	---	---	---	capture			Silent	SNP	18835332	18835332	7297	7	C	A	A	22	22	HDAC9	A	3	3
STARD3NL	83930	broad.mit.edu	36	7	38213668	38213668	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:38213668C>A	uc003tfr.1	+	c.38C>A	c.(37-39)ACC>AAC	p.T13N	STARD3NL_uc003tfs.1_Missense_Mutation_p.T13N|STARD3NL_uc003tft.1_Missense_Mutation_p.T13N	NM_032016	NP_114405	O95772	MENTO_HUMAN	MLN64 N-terminal homolog	13	Cytoplasmic (Potential).					integral to membrane|late endosome membrane				ovary(1)	1														0.284722	116.917656	122.906532	41	103	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38213668	38213668	15777	7	C	A	A	18	18	STARD3NL	A	3	3
RSPH10B	222967	broad.mit.edu	36	7	5934484	5934484	+	Silent	SNP	G	C	C			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:5934484G>C	uc003sph.1	-	c.2301C>G	c.(2299-2301)GTC>GTG	p.V767V	RSPH10B_uc003spg.1_Intron|RSPH10B_uc010ktd.1_Silent_p.V767V	NM_173565	NP_775836	B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B	767											0		Ovarian(82;0.0694)												0.137738	250.692997	364.056021	123	770	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)	Silent	SNP	5934484	5934484	14183	7	G	C	C	33	33	RSPH10B	C	3	3
COL1A2	1278	broad.mit.edu	36	7	93878152	93878152	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:93878152C>T	uc003ung.1	+	c.1213C>T	c.(1213-1215)CGT>TGT	p.R405C		NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen	405					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging			central_nervous_system(3)|ovary(2)	5	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)				Collagenase(DB00048)									0.246231	121.676657	133.344526	49	150	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.0031)		Missense_Mutation	SNP	93878152	93878152	3816	7	C	T	T	31	31	COL1A2	T	1	1
CSMD1	64478	broad.mit.edu	36	8	3876933	3876933	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0211-01	TCGA-06-0211-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:3876933C>T	uc010lrh.1	-	c.512G>A	c.(511-513)TGC>TAC	p.C171Y		NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	171	Extracellular (Potential).|Sushi 1.					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)												0.551181	196.93579	197.222677	70	57	CC		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	3876933	3876933	4085	8	C	T	T	25	25	CSMD1	T	2	2
GABBR2	9568	broad.mit.edu	36	9	100187842	100187842	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:100187842G>C	uc004ays.1	-	c.1563C>G	c.(1561-1563)AAC>AAG	p.N521K		NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51	521	Cytoplasmic (Potential).				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)									0.486486	197.350137	197.36768	54	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100187842	100187842	6407	9	G	C	C	44	44	GABBR2	C	3	3
TLR4	7099	broad.mit.edu	36	9	119515484	119515484	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:119515484G>C	uc004bjz.1	+	c.1257G>C	c.(1255-1257)TTG>TTC	p.L419F	TLR4_uc004bka.1_Missense_Mutation_p.L379F|TLR4_uc004bkb.1_Missense_Mutation_p.L219F	NM_138554	NP_612564	O00206	TLR4_HUMAN	toll-like receptor 4 precursor	419	LRR 12.|Extracellular (Potential).				activation of MAPK activity|cellular response to mechanical stimulus|defense response to Gram-negative bacterium|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of inflammatory response|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm	lipopolysaccharide receptor activity|transmembrane receptor activity			ovary(4)	4										157				0.380117	207.636746	209.791642	65	106	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119515484	119515484	16483	9	G	C	C	47	47	TLR4	C	3	3
MAGEB1	4112	broad.mit.edu	36	X	30178560	30178560	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0211-01	TCGA-06-0211-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30178560G>A	uc004dcc.1	+	c.29G>A	c.(28-30)CGT>CAT	p.R10H	MAGEB1_uc004dcd.1_Missense_Mutation_p.R10H|MAGEB1_uc004dce.1_Missense_Mutation_p.R10H|MAGEB1_uc010ngh.1_Missense_Mutation_p.R10H	NM_002363	NP_803134	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	10											0														0.954545	70.036784	72.444275	21	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30178560	30178560	9553	23	G	A	A	40	40	MAGEB1	A	1	1
CXorf22	170063	broad.mit.edu	36	X	35879926	35879926	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0211-01	TCGA-06-0211-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:35879926T>A	uc004ddj.1	+	c.971T>A	c.(970-972)ATT>AAT	p.I324N	CXorf22_uc010ngv.1_Non-coding_Transcript	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	324										large_intestine(1)|lung(1)|ovary(1)	3														0.854545	165.7624	172.413482	47	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35879926	35879926	4262	23	T	A	A	52	52	CXorf22	A	4	4
KRT24	192666	broad.mit.edu	36	17	36113248	36113248	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-0211-01	TCGA-06-0211-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:36113248_36113248delC	uc002hvd.1	-	c.224_224delG	c.(223-225)GGTfs	p.G75fs		NM_019016	NP_061889	Q2M2I5	K1C24_HUMAN	keratin 24	75	Head.|Gly-rich.					cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.00526)				GBM(61;380 1051 14702 23642 31441)								0.45			77	96				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	36113248	36113248	8776	17	C	-	-	18	18	KRT24	-	5	5
