{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T13:08:58Z","timestamp":1781269738614,"version":"3.54.1"},"reference-count":109,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,10,23]],"date-time":"2020-10-23T00:00:00Z","timestamp":1603411200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Natural Science Fundation for Distinguished Young Scholars of Heilongjiang Province of China","award":["JQ2020C004"],"award-info":[{"award-number":["JQ2020C004"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81572341"],"award-info":[{"award-number":["81572341"]}],"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":["61601150"],"award-info":[{"award-number":["61601150"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010722","name":"Harbin Medical University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010722","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fundamental Research Funds","award":["JFXN201912"],"award-info":[{"award-number":["JFXN201912"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http:\/\/www.licpathway.net\/VARAdb\/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include \u2018Variation information\u2019, \u2018Regulatory information\u2019, \u2018Related genes\u2019, \u2018Chromatin accessibility\u2019\u00a0and \u2018Chromatin interaction\u2019. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.<\/jats:p>","DOI":"10.1093\/nar\/gkaa922","type":"journal-article","created":{"date-parts":[[2020,10,22]],"date-time":"2020-10-22T11:10:40Z","timestamp":1603365040000},"page":"D1431-D1444","source":"Crossref","is-referenced-by-count":43,"title":["VARAdb: a comprehensive variation annotation database for human"],"prefix":"10.1093","volume":"49","author":[{"given":"Qi","family":"Pan","sequence":"first","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue-Juan","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xue-Feng","family":"Bai","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Le","family":"Han","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Ai","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan-Shan","family":"Shi","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming-Cong","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue-Zhu","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia-Xin","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xue-Cang","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guo-Rui","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiu-Yu","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University. 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Genet."},{"key":"2021010313132592700_B27","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":"2021010313132592700_B28","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"Genomes Project, C.","year":"2012","journal-title":"Nature"},{"key":"2021010313132592700_B29","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313132592700_B30","doi-asserted-by":"crossref","first-page":"D869","DOI":"10.1093\/nar\/gkv1317","article-title":"GWASdb v2: an update database for human genetic variants identified by genome-wide association studies","volume":"44","author":"Li","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2021010313132592700_B31","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/ng0504-431","article-title":"The genetic association database","volume":"36","author":"Becker","year":"2004","journal-title":"Nat. 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The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","author":"Consortium","year":"2015","journal-title":"Science"},{"key":"2021010313132592700_B35","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":"2021010313132592700_B36","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2021010313132592700_B37","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1002\/cphg.59","article-title":"PLINK: Key Functions for Data Analysis","volume":"97","author":"Slifer","year":"2018","journal-title":"Curr. Protoc. Hum. Genet."},{"key":"2021010313132592700_B38","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1101\/gr.097857.109","article-title":"Detection of nonneutral substitution rates on mammalian phylogenies","volume":"20","author":"Pollard","year":"2010","journal-title":"Genome Res."},{"key":"2021010313132592700_B39","doi-asserted-by":"crossref","first-page":"D1044","DOI":"10.1093\/nar\/gky1139","article-title":"OncoBase: a platform for decoding regulatory somatic mutations in human cancers","volume":"47","author":"Li","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313132592700_B40","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":"2021010313132592700_B41","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":"2021010313132592700_B42","doi-asserted-by":"crossref","first-page":"D252","DOI":"10.1093\/nar\/gkx1106","article-title":"HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis","volume":"46","author":"Kulakovskiy","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021010313132592700_B43","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. 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