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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	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	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
MST1P2	11209	broad.mit.edu	37	1	16974955	16974955	+	RNA	SNP	A	G	G	rs149751487	by1000genomes	TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr1:16974955A>G	uc010och.1	+	7		c.1415A>G			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						GCATGCTTTGATGTCTGGGAC	0.657000													8	63	---	---	---	---	0	0	0.080935	0	0
ZC3H11A	9877	broad.mit.edu	37	1	203816376	203816376	+	Silent	SNP	C	T	T			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr1:203816376C>T	uc001hac.2	+	15	1723	c.1107C>T	c.(1105-1107)GCC>GCT	p.A369A	ZC3H11A_uc001had.2_Silent_p.A369A|ZC3H11A_uc001hae.2_Silent_p.A369A|ZC3H11A_uc001haf.2_Silent_p.A369A|ZC3H11A_uc010pqm.1_Silent_p.A315A|ZC3H11A_uc001hag.1_Silent_p.A369A	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	369	Potential.						nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TTGAAAGAGCCAGTCAGAAAC	0.373000													7	38	---	---	---	---	0	0	0.038147	0	0
LOC650368	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	T	T			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr11:3427845C>T	uc010qxs.1	+	9		c.838C>T			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						CTTCAAGTGGCAGGAGCAGAA	0.587000													7	42	---	---	---	---	0	0	0.029380	0	0
NPAT	4863	broad.mit.edu	37	11	108032299	108032299	+	Missense_Mutation	SNP	A	G	G			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr11:108032299A>G	uc001pjz.3	-	17	3616	c.3514T>C	c.(3514-3516)TGC>CGC	p.C1172R	NPAT_uc010rvv.1_Missense_Mutation_p.C228R	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	1172					positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|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)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		ACATCGCTGCATAATTCATTC	0.363000													18	153	---	---	---	---	0	0	0.175082	0	0
ELP2	55250	broad.mit.edu	37	18	33736468	33736468	+	Missense_Mutation	SNP	T	C	C			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr18:33736468T>C	uc002kzk.1	+	13	1325	c.1315T>C	c.(1315-1317)TAT>CAT	p.Y439H	ELP2_uc010xcg.1_Missense_Mutation_p.Y504H|ELP2_uc002kzl.1_RNA|ELP2_uc002kzm.1_Missense_Mutation_p.Y413H|ELP2_uc010xch.1_Missense_Mutation_p.Y434H|ELP2_uc002kzn.1_Missense_Mutation_p.Y369H|ELP2_uc002kzo.1_Missense_Mutation_p.Y369H	NM_018255	NP_060725	Q6IA86	ELP2_HUMAN	elongator protein 2	439	WD 9.				regulation of transcription from RNA polymerase II promoter	Golgi apparatus|transcription elongation factor complex				breast(2)|ovary(1)|skin(1)	4						GATACATGGGTATGACCTGAA	0.378000													5	92	---	---	---	---	0	0	0.184627	0	0
Unknown	0	broad.mit.edu	37	22	20295379	20295379	+	RNA	SNP	C	T	T			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr22:20295379C>T	uc002zrw.1	+	2		c.2859C>T								Homo sapiens mRNA for KIAA1653 protein, partial cds.																		GGGGCCAAGCCGGTGCGGGGC	0.612000													3	18	---	---	---	---	0	0	0.115264	0	0
SPDYE7P	441251	broad.mit.edu	37	7	72339511	72339511	+	RNA	SNP	A	C	C			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr7:72339511A>C	uc010lal.1	-	1		c.145T>G				NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0						CCACCACTCCATCTTCCTTTT	0.582000													3	27	---	---	---	---	0	0	0.150653	0	0
TUBBP5	643224	broad.mit.edu	37	9	141071154	141071154	+	Missense_Mutation	SNP	T	C	C	rs150819761	by1000genomes	TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr9:141071154T>C	uc004com.2	+	4	818	c.557T>C	c.(556-558)GTC>GCC	p.V186A	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						GTGAACATGGTCCCGTTTCCC	0.632000													4	69	---	---	---	---	0	0	0.047766	0	0
BCL9	607	broad.mit.edu	37	1	147091501	147091501	+	Frame_Shift_Del	DEL	C	-	-			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr1:147091501delC	uc001epq.2	+	8	2280	c.1540delC	c.(1540-1542)CCCfs	p.P514fs	BCL9_uc010ozr.1_Frame_Shift_Del_p.P440fs	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	514	Poly-Pro.|Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					GGTCCGAGGACCCCCCCCTCC	0.582			T	IGH@|IGL@	B-ALL								7	161	---	---	---	---					
Unknown	0	broad.mit.edu	37	1	248844550	248844550	+	IGR	DEL	T	-	-			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr1:248844550delT								OR2T27 (30365 upstream) : OR14I1 (120 downstream)																							ATTCAACAGGTTTTTTTTTTC	0.264													3	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	10	134206066	134206068	+	IGR	DEL	TGG	-	-	rs72458419		TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr10:134206066_134206068delTGG								LRRC27 (11056 upstream) : PWWP2B (4634 downstream)																							gtggtggtaatggtgatgatggt	0.000													2	4	---	---	---	---					
MED4	29079	broad.mit.edu	37	13	48669345	48669345	+	5'Flank	DEL	G	-	-			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr13:48669345delG	uc001vby.1	-						MED4_uc010tge.1_5'Flank|MED4_uc010tgf.1_5'Flank	NM_014166	NP_054885	Q9NPJ6	MED4_HUMAN	mediator complex subunit 4						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)		CGCCCCCTTTGGGCCTGGAGG	0.667											OREG0022406	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	6	---	---	---	---					
MESP2	145873	broad.mit.edu	37	15	90320121	90320144	+	In_Frame_Del	DEL	AGGGGCAGGGGCAAGGGCAGGGGC	-	-	rs66601910		TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr15:90320121_90320144delAGGGGCAGGGGCAAGGGCAGGGGC	uc002bon.2	+	1	533_556	c.533_556delAGGGGCAGGGGCAAGGGCAGGGGC	c.(532-558)GAGGGGCAGGGGCAAGGGCAGGGGCAG>GAG	p.GQGQGQGQ195del	MESP2_uc010uqa.1_Intron	NM_001039958	NP_001035047	Q0VG99	MESP2_HUMAN	mesoderm posterior 2 homolog	195_202	13 X 2 AA tandem repeats of G-Q.|12.			Missing (in Ref. 2; AAI11414).	Notch signaling pathway	nucleus	DNA binding				0	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			ACGCaggcggaggggcaggggcaagggcaggggcaggggcaggg	0.473													4	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	58511029	58511029	+	IGR	DEL	C	-	-	rs59873900	by1000genomes	TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr17:58511029delC								C17orf64 (2243 upstream) : APPBP2 (9491 downstream)																							tttTCTTTTTCTTTTTTTTTC	0.184													7	8	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	20634038	20634039	+	IGR	DEL	TG	-	-			TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr19:20634038_20634039delTG								ZNF826 (26276 upstream) : ZNF737 (86760 downstream)																							TTAGTAAAAATGTGTGTGTGTG	0.401													7	57	---	---	---	---					
CDC45	8318	broad.mit.edu	37	22	19466757	19466758	+	5'Flank	INS	-	G	G	rs140179780	by1000genomes	TCGA-ET-A39L-01A-12D-A19J-08	TCGA-ET-A39L-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	7ca36d05-5efa-4fbe-8d3c-c57e8f77b6d4	09a340d3-3d5f-4a47-892c-5139c0bb78d3	g.chr22:19466757_19466758insG	uc002zpr.2	+						UFD1L_uc002zpm.2_5'Flank|UFD1L_uc002zpo.2_5'Flank|UFD1L_uc011agy.1_5'Flank|UFD1L_uc002zpp.2_5'Flank|UFD1L_uc010grq.2_5'Flank|CDC45_uc011agz.1_5'Flank|CDC45_uc011aha.1_5'Flank|CDC45_uc002zps.2_5'Flank|CDC45_uc002zpt.2_5'Flank	NM_003504	NP_003495	O75419	CDC45_HUMAN	CDC45-like						DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1						CGAGACCCGGAGGGGGGGTGCC	0.653													2	4	---	---	---	---					
