[{"type":"categorical","name":"chromHMM of GM12878","url":"http://egg.wustl.edu/d/hg19/E116_15_coreMarks_dense.gz","mode":1,"qtc":{"anglescale":1,"height":25,"bg":"rgb(240,240,240)"},"metadata":{"md1":["13047"],"md3":["27004"],"md4":["30003"]},"categories":{"1":["Active TSS","#ff0000"],"2":["Flanking Active TSS","#ff4500"],"3":["Transcr at gene 5' and 3'","#32cd32"],"4":["Strong transcription","#008000"],"5":["Weak transcription","#006400"],"6":["Genic enhancers","#c2e105"],"7":["Enhancers","#ffff00"],"8":["ZNF genes & repeats","#66cdaa"],"9":["Heterochromatin","#8a91d0"],"10":["Bivalent/Poised TSS","#cd5c5c"],"11":["Flanking Bivalent TSS/Enh","#e9967a"],"12":["Bivalent Enhancer","#bdb76b"],"13":["Repressed PolyComb","#808080"],"14":["Weak Repressed PolyComb","#c0c0c0"],"15":["Quiescent/Low","#ffffff"],"-1":["no information","transparent"]}},{"type":"interaction","name":"HiC.GM12878","url":"http://egg.wustl.edu/d/hg19/GSE62742_HiC.GM12878.correlations.sort.gz","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":7223,"ncolorscore":0,"pfilterscore":3500,"nfilterscore":0,"height":10},"metadata":{"md1":["13047"],"md3":["27003"],"md4":["30018"]},"details":{"Publication":"Grubert F, Zaugg JB, Kasowski M, Ursu O et al. Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell 2015 Aug 27;162(5):1051-65.","PMID":"26300125"},"geolst":["GSE62742"]},{"type":"hic","name":"GM12878_9ENCODE_Batch2_HIC049","url":"https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/HIC049.hic","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":57.93536,"ncolorscore":0,"pfilterscore":25,"nfilterscore":0,"height":50,"unit_res":"BP","matrix":"oe","norm":"KR","bin_size":10000,"d_binsize":10000,"hasChr":0},"metadata":{"md1":["13047"],"md3":["27003"]}},{"type":"hic","name":"GM12878_8ENCODE_Batch1_HIC048","url":"https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/HIC048.hic","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":15.024314,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50,"unit_res":"BP","matrix":"oe","norm":"KR","bin_size":50000,"d_binsize":50000,"hasChr":0},"metadata":{"md1":["13047"],"md3":["27003"]}},{"type":"hic","name":"GM12878_7no_Xlink_1combined","url":"https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_noXlink.hic","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":6.1037693,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50,"unit_res":"BP","matrix":"oe","norm":"KR","bin_size":50000,"d_binsize":50000,"hasChr":0},"metadata":{"md1":["13047"],"md3":["27003"]}},{"type":"hic","name":"GM12878_6in_situ_DpnII_1combined","url":"https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_DpnII.hic","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":9.617931,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50,"unit_res":"BP","matrix":"oe","norm":"KR","bin_size":0,"d_binsize":50000,"hasChr":0},"metadata":{"md1":["13047"],"md3":["27003"]}},{"type":"hic","name":"GM12878_5dilution_1combined","url":"https://hicfiles.s3.amazonaws.com/hiseq/gm12878/dilution/combined.hic","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":5.204477,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50,"unit_res":"BP","matrix":"oe","norm":"KR","bin_size":0,"d_binsize":50000,"hasChr":0},"metadata":{"md1":["13047"],"md3":["27003"]}},{"type":"hic","name":"GM12878_4supernatant_HIC033","url":"https://hicfiles.s3.amazonaws.com/hiseq/gm12878/supernatant/HIC033.hic","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":24.55506,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50,"unit_res":"BP","matrix":"oe","norm":"KR","bin_size":0,"d_binsize":50000,"hasChr":0},"metadata":{"md1":["13047"],"md3":["27003"]}},{"type":"hic","name":"2011Kalhor_TCC_combined","url":"http://hicfiles.s3.amazonaws.com/external/kalhor/tcc-combined.hic","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":12.600089,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50,"unit_res":"BP","matrix":"oe","norm":"KR","bin_size":0,"d_binsize":50000,"hasChr":0},"metadata":{"md1":["13047"],"md3":["27003"]}},{"type":"interaction","name":"HiC GM12878 25Kb KR norm","url":"http://epgg-test.wustl.edu/dli/long-range-test/dli/GM12878_combined_25kb_resolution_intrachromosomal.processed.KRnorm.sort.gz","mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":0,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":10},"metadata":{"md1":["13047"],"md3":["27003"],"md4":["30022"]},"details":{"Publication":"Rao SS, Huntley MH, Durand NC, Stamenova EK et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 2014 Dec 18;159(7):1665-80.","PMID":"25497547"},"geolst":["GSE63525"]},{"type":"native_track","list":[{"name":"refGene","mode":3,"qtc":{"anglescale":1,"pr":255,"pg":0,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":50,"summeth":1,"textcolor":"#000000","fontsize":"8pt","fontfamily":"sans-serif","fontbold":true,"bedcolor":"#002EB8"},"metadata":{},"details":{"source":"UCSC Genome Browser","download date":"Jan 1, 2012"}},{"name":"rmsk_all","mode":7,"qtc":{"anglescale":1,"pr":255,"pg":0,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":35,"summeth":1,"textcolor":"#000000","fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"bedcolor":"#336666"},"showscoreidx":2,"scorenamelst":["Smith-Waterman score","SW score normalized by length","1-divergence%"],"scorescalelst":[{"type":0},{"type":0},{"type":0}],"metadata":{},"categories":{"1":["SINE - short interspersed nuclear elements","#cc0000"],"2":["LINE - long interspersed nuclear element","#FF6600"],"3":["LTR - long terminal repeat element","#006600"],"4":["DNA transposon","#4A72E8"],"5":["Simple repeat, micro-satellite","#AB833B"],"6":["Satellite repeat","#660000"],"7":["Low complexity repeat","#663333"],"8":["RNA repeat","#cc33ff"],"9":["Other repeats","#488E8E"],"10":["Unknown","#5C5C5C"],"-1":["no information","transparent"]}}]},{"type":"bedgraph","name":"CD8 Naive Primary cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E047.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13021"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"CD4 Naive Primary cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E038.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13025"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"CD4 Memory Primary cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E037.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13020"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Breast vHMEC methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E028.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13007"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Breast Myoepithelial cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E027.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13005"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"H1 methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E003.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["11101"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Neurospheres  Cortex Derived methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E053.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13033"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Neurospheres  Ganglionic Eminence Derived methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E054.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13031"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Penis Foreskin Fibroblast Primary Cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E055.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13144"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Penis Foreskin Fibroblast Primary Cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E056.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13144"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Penis Foreskin Keratinocyte Primary Cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E057.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13035"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Penis Foreskin Keratinocyte Primary Cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E058.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13035"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Penis Foreskin Melanocyte Primary Cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E059.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13145"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Penis Foreskin Melanocyte Primary Cells methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E061.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["13145"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Fetal Brain methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E081.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["12003"],"md3":["21006"],"md4":["30025"]}},{"type":"bedgraph","name":"Fetal Brain methylCRF","url":"http://remc.wustl.edu/dli/mCRF/E082.fm.bedGraph.gz","mode":"hide","qtc":{"barplotbg":"#c0c0c0","pr":179,"pg":0,"pb":45,"pth":"rgb(125,0,31)","thtype":1,"thmin":0,"thmax":1,"height":30},"metadata":{"md1":["12003"],"md3":["21006"],"md4":["30025"]}},{"type":"metadata","vocabulary_set":{"md1":"http://vizhub.wustl.edu/metadata/human/Samples","md2":"http://vizhub.wustl.edu/metadata/human/Donor","md3":"http://vizhub.wustl.edu/metadata/Experimental_assays","md4":"http://vizhub.wustl.edu/metadata/Institutions"},"show_terms":{"md1":["Sample"],"md3":["Assay"]}},{"type":"coordinate_override","coord":"chr13,34674006,chr13,36272804"}]