{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T02:41:36Z","timestamp":1772851296680,"version":"3.50.1"},"reference-count":102,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2018,11,16]],"date-time":"2018-11-16T00:00:00Z","timestamp":1542326400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key R&D Program of China","award":["2016YFC0900400"],"award-info":[{"award-number":["2016YFC0900400"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81490753"],"award-info":[{"award-number":["81490753"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81502150"],"award-info":[{"award-number":["81502150"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National 973 Program","award":["2015CB553904"],"award-info":[{"award-number":["2015CB553904"]}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2018M641117"],"award-info":[{"award-number":["2018M641117"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,8]]},"DOI":"10.1093\/nar\/gky1139","type":"journal-article","created":{"date-parts":[[2018,11,12]],"date-time":"2018-11-12T20:07:49Z","timestamp":1542053269000},"page":"D1044-D1055","source":"Crossref","is-referenced-by-count":45,"title":["OncoBase: a platform for decoding regulatory somatic mutations in human cancers"],"prefix":"10.1093","volume":"47","author":[{"given":"Xianfeng","family":"Li","sequence":"first","affiliation":[{"name":"Key laboratory of Carcinogenesis and Translational Research (Ministry of Education\/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China"},{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Leisheng","family":"Shi","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"Key laboratory of Carcinogenesis and Translational Research (Ministry of Education\/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China"}]},{"given":"Jianing","family":"Zhong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000,China"}]},{"given":"Xiaolu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA"}]},{"given":"Huajing","family":"Teng","sequence":"additional","affiliation":[{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Xiaohui","family":"Shi","sequence":"additional","affiliation":[{"name":"Sino-Danish college, University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Haonan","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA"}]},{"given":"Shasha","family":"Ruan","sequence":"additional","affiliation":[{"name":"Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430072, China"}]},{"given":"MingKun","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Zhong Sheng","family":"Sun","sequence":"additional","affiliation":[{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Qimin","family":"Zhan","sequence":"additional","affiliation":[{"name":"Key laboratory of Carcinogenesis and Translational Research (Ministry of Education\/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0852-4266","authenticated-orcid":false,"given":"Fengbiao","family":"Mao","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,11,16]]},"reference":[{"key":"key\n\t\t\t\t2019010803581827700_B1","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1038\/ng.3539","article-title":"Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin","volume":"48","author":"Whalen","year":"2016","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B2","doi-asserted-by":"crossref","first-page":"7793","DOI":"10.1093\/nar\/gky678","article-title":"Performance evaluation of pathogenicity-computation methods for missense variants","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B3","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature13176","article-title":"Identification of genomic alterations in oesophageal squamous cell cancer","volume":"509","author":"Song","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B4","doi-asserted-by":"crossref","first-page":"3349","DOI":"10.3892\/or.2016.4738","article-title":"Whole-exome sequencing identifies a somatic missense mutation of NBN in clear cell sarcoma of the salivary gland","volume":"35","author":"Zhang","year":"2016","journal-title":"Oncol. Rep."},{"key":"key\n\t\t\t\t2019010803581827700_B5","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1038\/ng.3101","article-title":"Genome-wide analysis of noncoding regulatory mutations in cancer","volume":"46","author":"Weinhold","year":"2014","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B6","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature09906","article-title":"Mapping and analysis of chromatin state dynamics in nine human cell types","volume":"473","author":"Ernst","year":"2011","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B7","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1038\/ng.3404","article-title":"Partitioning heritability by functional annotation using genome-wide association summary statistics","volume":"47","author":"Finucane","year":"2015","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B8","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1126\/science.1229259","article-title":"Highly recurrent TERT promoter mutations in human melanoma","volume":"339","author":"Huang","year":"2013","journal-title":"Science"},{"key":"key\n\t\t\t\t2019010803581827700_B9","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1126\/science.1230062","article-title":"TERT promoter mutations in familial and sporadic melanoma","volume":"339","author":"Horn","year":"2013","journal-title":"Science"},{"key":"key\n\t\t\t\t2019010803581827700_B10","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1016\/j.ejca.2015.03.010","article-title":"Recurrent TERT promoter mutations identified in a large-scale study of multiple tumour types are associated with increased TERT expression and telomerase activation","volume":"51","author":"Huang","year":"2015","journal-title":"Eur. J. Cancer"},{"key":"key\n\t\t\t\t2019010803581827700_B11","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1002\/path.5005","article-title":"Genetic landscape of papillary thyroid carcinoma in the Chinese population","volume":"244","author":"Liang","year":"2018","journal-title":"J. Pathol."},{"key":"key\n\t\t\t\t2019010803581827700_B12","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1038\/ng.3141","article-title":"Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types","volume":"46","author":"Fredriksson","year":"2014","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B13","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1093\/annonc\/mdv561","article-title":"Beyond the exome: the role of non-coding somatic mutations in cancer","volume":"27","author":"Piraino","year":"2016","journal-title":"Ann. Oncol."},{"key":"key\n\t\t\t\t2019010803581827700_B14","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nrg.2015.17","article-title":"Role of non-coding sequence variants in cancer","volume":"17","author":"Khurana","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B15","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.1101\/gr.137323.112","article-title":"Annotation of functional variation in personal genomes using RegulomeDB","volume":"22","author":"Boyle","year":"2012","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010803581827700_B16","doi-asserted-by":"crossref","first-page":"D930","DOI":"10.1093\/nar\/gkr917","article-title":"HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants","volume":"40","author":"Ward","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B17","doi-asserted-by":"crossref","first-page":"D877","DOI":"10.1093\/nar\/gkv1340","article-title":"HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease","volume":"44","author":"Ward","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B18","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/s13073-018-0565-y","article-title":"Prioritization and functional assessment of noncoding variants associated with complex diseases","volume":"10","author":"Zhou","year":"2018","journal-title":"Genome Med"},{"key":"key\n\t\t\t\t2019010803581827700_B19","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1186\/s13059-014-0480-5","article-title":"FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer","volume":"15","author":"Fu","year":"2014","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t2019010803581827700_B20","doi-asserted-by":"crossref","first-page":"bav124","DOI":"10.1093\/database\/bav124","article-title":"CCSI: a database providing chromatin-chromatin spatial interaction information","volume":"2016","author":"Xie","year":"2016","journal-title":"Database (Oxford)"},{"key":"key\n\t\t\t\t2019010803581827700_B21","doi-asserted-by":"crossref","first-page":"D643","DOI":"10.1093\/nar\/gkw1022","article-title":"3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes","volume":"45","author":"Lu","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B22","doi-asserted-by":"crossref","first-page":"W150","DOI":"10.1093\/nar\/gkt456","article-title":"GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications","volume":"41","author":"Li","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B23","doi-asserted-by":"crossref","first-page":"W114","DOI":"10.1093\/nar\/gky407","article-title":"GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits","volume":"46","author":"Huang","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B24","doi-asserted-by":"crossref","first-page":"D52","DOI":"10.1093\/nar\/gkx1017","article-title":"3DIV: A 3D-genome Interaction Viewer and database","volume":"46","author":"Yang","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B25","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/j.cell.2017.01.018","article-title":"Clonal heterogeneity and tumor evolution: past, present, and the future","volume":"168","author":"McGranahan","year":"2017","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803581827700_B26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41525-017-0040-5","article-title":"Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival","volume":"3","author":"Hornshoj","year":"2018","journal-title":"NPJ Genomic Med."},{"key":"key\n\t\t\t\t2019010803581827700_B27","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1126\/science.1105136","article-title":"The ENCODE (ENCyclopedia Of DNA Elements) Project","volume":"306","author":"Consortium, E.P.","year":"2004","journal-title":"Science"},{"key":"key\n\t\t\t\t2019010803581827700_B28","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nbt1010-1045","article-title":"The NIH roadmap epigenomics mapping consortium","volume":"28","author":"Bernstein","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t2019010803581827700_B29","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/ng1966","article-title":"Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome","volume":"39","author":"Heintzman","year":"2007","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B30","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1038\/nature07730","article-title":"ChIP-seq accurately predicts tissue-specific activity of enhancers","volume":"457","author":"Visel","year":"2009","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B31","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature07829","article-title":"Histone modifications at human enhancers reflect global cell-type-specific gene expression","volume":"459","author":"Heintzman","year":"2009","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B32","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1002\/jcb.22116","article-title":"ChIP-based methods for the identification of long-range chromatin interactions","volume":"107","author":"Fullwood","year":"2009","journal-title":"J. Cell. Biochem."},{"key":"key\n\t\t\t\t2019010803581827700_B33","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1101\/gr.074906.107","article-title":"Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses","volume":"19","author":"Fullwood","year":"2009","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010803581827700_B34","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nature11279","article-title":"The long-range interaction landscape of gene promoters","volume":"489","author":"Sanyal","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B35","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"key\n\t\t\t\t2019010803581827700_B36","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803581827700_B37","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B38","doi-asserted-by":"crossref","first-page":"2042","DOI":"10.1016\/j.celrep.2016.10.061","article-title":"A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome","volume":"17","author":"Schmitt","year":"2016","journal-title":"Cell Rep."},{"key":"key\n\t\t\t\t2019010803581827700_B39","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/ng.3286","article-title":"Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C","volume":"47","author":"Mifsud","year":"2015","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B40","doi-asserted-by":"crossref","first-page":"1854","DOI":"10.1101\/gr.175034.114","article-title":"Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C","volume":"24","author":"Dryden","year":"2014","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010803581827700_B41","doi-asserted-by":"crossref","first-page":"10069","DOI":"10.1038\/ncomms10069","article-title":"Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci","volume":"6","author":"Martin","year":"2015","journal-title":"Nat. Commun."},{"key":"key\n\t\t\t\t2019010803581827700_B42","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/nature13138","article-title":"Obesity-associated variants within FTO form long-range functional connections with IRX3","volume":"507","author":"Smemo","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B43","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1016\/j.cell.2016.09.037","article-title":"Lineage-Specific genome architecture links enhancers and non-coding disease variants to target gene promoters","volume":"167","author":"Javierre","year":"2016","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803581827700_B44","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1016\/j.cell.2015.04.013","article-title":"Widespread macromolecular interaction perturbations in human genetic disorders","volume":"161","author":"Sahni","year":"2015","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803581827700_B45","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1038\/nmeth.2651","article-title":"Network-based stratification of tumor mutations","volume":"10","author":"Hofree","year":"2013","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t2019010803581827700_B46","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The Cancer Genome Atlas Pan-Cancer analysis project","volume":"45","author":"Cancer Genome Atlas Research, N.","year":"2013","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B47","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nature08987","article-title":"International network of cancer genome projects","volume":"464","author":"International Cancer Genome, C.","year":"2010","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B48","doi-asserted-by":"crossref","first-page":"D945","DOI":"10.1093\/nar\/gkq929","article-title":"COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in Cancer","volume":"39","author":"Forbes","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B49","doi-asserted-by":"crossref","first-page":"D862","DOI":"10.1093\/nar\/gkv1222","article-title":"ClinVar: public archive of interpretations of clinically relevant variants","volume":"44","author":"Landrum","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B50","doi-asserted-by":"crossref","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","article-title":"ClinVar: public archive of relationships among sequence variation and human phenotype","volume":"42","author":"Landrum","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B51","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B52","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t2019010803581827700_B53","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1038\/nprot.2017.124","article-title":"Chromatin-state discovery and genome annotation with ChromHMM","volume":"12","author":"Ernst","year":"2017","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t2019010803581827700_B54","doi-asserted-by":"crossref","first-page":"D195","DOI":"10.1093\/nar\/gks1089","article-title":"HOCOMOCO: a comprehensive collection of human transcription factor binding sites models","volume":"41","author":"Kulakovskiy","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B55","doi-asserted-by":"crossref","first-page":"D171","DOI":"10.1093\/nar\/gks1221","article-title":"Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium","volume":"41","author":"Wang","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B56","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"key\n\t\t\t\t2019010803581827700_B57","doi-asserted-by":"crossref","first-page":"2976","DOI":"10.1093\/nar\/gkt1249","article-title":"Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments","volume":"42","author":"Kheradpour","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B58","doi-asserted-by":"crossref","first-page":"3847","DOI":"10.1093\/bioinformatics\/btv470","article-title":"motifbreakR: an R\/Bioconductor package for predicting variant effects at transcription factor binding sites","volume":"31","author":"Coetzee","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581827700_B59","doi-asserted-by":"crossref","first-page":"D613","DOI":"10.1093\/nar\/gkp939","article-title":"The UCSC Genome Browser database: update 2010","volume":"38","author":"Rhead","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B60","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1038\/s41467-018-03113-2","article-title":"Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus","volume":"9","author":"Zhang","year":"2018","journal-title":"Nat. Commun."},{"key":"key\n\t\t\t\t2019010803581827700_B61","doi-asserted-by":"crossref","first-page":"10812","DOI":"10.1038\/ncomms10812","article-title":"Constructing 3D interaction maps from 1D epigenomes","volume":"7","author":"Zhu","year":"2016","journal-title":"Nat. Commun."},{"key":"key\n\t\t\t\t2019010803581827700_B62","doi-asserted-by":"crossref","first-page":"2727","DOI":"10.1093\/bioinformatics\/btw375","article-title":"4DGenome: a comprehensive database of chromatin interactions","volume":"32","author":"Teng","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581827700_B63","doi-asserted-by":"crossref","first-page":"3543","DOI":"10.1093\/bioinformatics\/btw495","article-title":"EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell\/tissue types","volume":"32","author":"Gao","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581827700_B64","doi-asserted-by":"crossref","first-page":"D164","DOI":"10.1093\/nar\/gkv1002","article-title":"dbSUPER: a database of super-enhancers in mouse and human genome","volume":"44","author":"Khan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B65","doi-asserted-by":"crossref","first-page":"D172","DOI":"10.1093\/nar\/gkv1243","article-title":"SEA: a super-enhancer archive","volume":"44","author":"Wei","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B66","doi-asserted-by":"crossref","first-page":"12611","DOI":"10.1093\/nar\/gkx1074","article-title":"Conserved non-coding elements: developmental gene regulation meets genome organization","volume":"45","author":"Polychronopoulos","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B67","doi-asserted-by":"crossref","first-page":"D101","DOI":"10.1093\/nar\/gks1092","article-title":"UCNEbase\u2013a database of ultraconserved non-coding elements and genomic regulatory blocks","volume":"41","author":"Dimitrieva","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B68","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1038\/ng.3950","article-title":"Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines","volume":"49","author":"Cao","year":"2017","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B69","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/database\/bax028","article-title":"GeneHancer: genome-wide integration of enhancers and target genes in GeneCards","volume":"2017","author":"Fishilevich","year":"2017","journal-title":"Database (Oxford)"},{"key":"key\n\t\t\t\t2019010803581827700_B70","doi-asserted-by":"crossref","first-page":"1740","DOI":"10.1093\/bioinformatics\/btw041","article-title":"BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications","volume":"32","author":"Cui","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581827700_B71","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gkv1308","article-title":"RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins","volume":"44","author":"Mao","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B72","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature24277","article-title":"Genetic effects on gene expression across human tissues","volume":"550","year":"2017","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B73","doi-asserted-by":"crossref","first-page":"D971","DOI":"10.1093\/nar\/gkx861","article-title":"PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types","volume":"46","author":"Gong","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B74","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1093\/bioinformatics\/btr678","article-title":"seeQTL: a searchable database for human eQTLs","volume":"28","author":"Xia","year":"2012","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581827700_B75","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1093\/bioinformatics\/btp644","article-title":"SCAN: SNP and copy number annotation","volume":"26","author":"Gamazon","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010803581827700_B76","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1038\/nature08872","article-title":"Understanding mechanisms underlying human gene expression variation with RNA sequencing","volume":"464","author":"Pickrell","year":"2010","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B77","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s13059-016-0926-z","article-title":"Systematic identification of genetic influences on methylation across the human life course","volume":"17","author":"Gaunt","year":"2016","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t2019010803581827700_B78","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/nature10808","article-title":"DNase I sensitivity QTLs are a major determinant of human expression variation","volume":"482","author":"Degner","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010803581827700_B79","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1016\/j.cell.2015.07.048","article-title":"Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions","volume":"162","author":"Grubert","year":"2015","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803581827700_B80","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/ncomms1396","article-title":"Ranking stability and super-stable nodes in complex networks","volume":"2","author":"Ghoshal","year":"2011","journal-title":"Nat. Commun."},{"key":"key\n\t\t\t\t2019010803581827700_B81","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkx918","article-title":"EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases","volume":"46","author":"Mao","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B82","first-page":"557","article-title":"PageRank as a function of the damping factor","author":"Paolo\u00a0Boldi","year":"2005","journal-title":"Proceedings of the 14th International Conference on World Wide Web"},{"key":"key\n\t\t\t\t2019010803581827700_B83","doi-asserted-by":"crossref","first-page":"D893","DOI":"10.1093\/nar\/gku943","article-title":"EpilepsyGene: a genetic resource for genes and mutations related to epilepsy","volume":"43","author":"Ran","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B84","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1136\/jmedgenet-2014-102656","article-title":"mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing","volume":"52","author":"Li","year":"2015","journal-title":"J. Med. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B85","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1038\/mp.2015.58","article-title":"Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database","volume":"21","author":"Li","year":"2016","journal-title":"Mol. Psychiatry"},{"key":"key\n\t\t\t\t2019010803581827700_B86","doi-asserted-by":"crossref","first-page":"D64","DOI":"10.1093\/nar\/gkx944","article-title":"CirGRDB: a database for the genome-wide deciphering circadian genes and regulators","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B87","doi-asserted-by":"crossref","first-page":"D1039","DOI":"10.1093\/nar\/gkx1039","article-title":"VarCards: an integrated genetic and clinical database for coding variants in the human genome","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B88","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1126\/science.1259037","article-title":"Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element","volume":"346","author":"Mansour","year":"2014","journal-title":"Science"},{"key":"key\n\t\t\t\t2019010803581827700_B89","doi-asserted-by":"crossref","first-page":"e1006773","DOI":"10.1371\/journal.pgen.1006773","article-title":"Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature","volume":"13","author":"Fredriksson","year":"2017","journal-title":"PLos Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B90","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.tig.2016.10.008","article-title":"Mining the unknown: assigning function to noncoding single nucleotide polymorphisms","volume":"33","author":"Nishizaki","year":"2017","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B91","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/nmeth.2832","article-title":"Functional annotation of noncoding sequence variants","volume":"11","author":"Ritchie","year":"2014","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t2019010803581827700_B92","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/nmeth.3547","article-title":"Predicting effects of noncoding variants with deep learning-based sequence model","volume":"12","author":"Zhou","year":"2015","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t2019010803581827700_B93","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1038\/ng.3331","article-title":"A method to predict the impact of regulatory variants from DNA sequence","volume":"47","author":"Lee","year":"2015","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B94","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nbt.3300","article-title":"Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning","volume":"33","author":"Alipanahi","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t2019010803581827700_B95","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/nmeth.3065","article-title":"Predicting the human epigenome from DNA motifs","volume":"12","author":"Whitaker","year":"2015","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t2019010803581827700_B96","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/ng.3810","article-title":"Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data","volume":"49","author":"Huang","year":"2017","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B97","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1038\/s41588-018-0160-6","article-title":"Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk","volume":"50","author":"Zhou","year":"2018","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B98","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010803581827700_B99","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/s41588-018-0091-2","article-title":"A global transcriptional network connecting noncoding mutations to changes in tumor gene expression","volume":"50","author":"Zhang","year":"2018","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010803581827700_B100","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.cell.2018.06.003","article-title":"Biology and clinical implications of the 19q13 aggressive prostate cancer susceptibility locus","volume":"174","author":"Gao","year":"2018","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010803581827700_B101","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1158\/2159-8290.CD-17-0532","article-title":"Somatic superenhancer duplications and hotspot mutations lead to oncogenic activation of the KLF5 transcription factor","volume":"8","author":"Zhang","year":"2018","journal-title":"Cancer Discov."},{"key":"key\n\t\t\t\t2019010803581827700_B102","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1126\/science.aaf7613","article-title":"High-resolution interrogation of functional elements in the noncoding genome","volume":"353","author":"Sanjana","year":"2016","journal-title":"Science"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/D1\/D1044\/27437499\/gky1139.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,7]],"date-time":"2023-09-07T00:43:26Z","timestamp":1694047406000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/D1\/D1044\/5184720"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,11,16]]},"references-count":102,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2018,11,16]]},"published-print":{"date-parts":[[2019,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky1139","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,1,8]]},"published":{"date-parts":[[2018,11,16]]}}}