{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T08:52:28Z","timestamp":1769244748544,"version":"3.49.0"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,9,27]],"date-time":"2021-09-27T00:00:00Z","timestamp":1632700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Chinese National Key Research and Development","award":["2018YFC1315600"],"award-info":[{"award-number":["2018YFC1315600"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070675"],"award-info":[{"award-number":["32070675"]}],"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":["31871327"],"award-info":[{"award-number":["31871327"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006606","name":"Natural Science Foundation of Tianjin","doi-asserted-by":"publisher","award":["19JCJQJC63600"],"award-info":[{"award-number":["19JCJQJC63600"]}],"id":[{"id":"10.13039\/501100006606","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Interpreting the molecular mechanism of genomic variations and their causal relationship with diseases\/traits are important and challenging problems in the human genetic study. To provide comprehensive and context-specific variant annotations for biologists and clinicians, here, by systematically integrating over 4TB genomic\/epigenomic profiles and frequently-used annotation databases from various biological domains, we develop a variant annotation database, called VannoPortal. In general, the database has following major features: (i)\u00a0systematically integrates 40 genome-wide variant annotations and prediction scores regarding allele frequency, linkage disequilibrium, evolutionary signature, disease\/trait association, tissue\/cell type-specific epigenome, base-wise functional prediction, allelic imbalance and pathogenicity; (ii) equips with our recent novel index system and parallel random-sweep searching algorithms for efficient management of backend databases and information extraction; (iii) greatly expands context-dependent variant annotation to incorporate large-scale epigenomic maps and regulatory profiles (such as EpiMap) across over 33 tissue\/cell types; (iv) compiles many genome-scale base-wise prediction scores for regulatory\/pathogenic variant classification beyond protein-coding region; (v) enables fast retrieval and direct comparison of functional evidence among linked variants using highly interactive web panel in addition to plain table; (vi) introduces many visualization functions for more efficient identification and interpretation of functional variants in single web page. VannoPortal is freely available at http:\/\/mulinlab.org\/vportal.<\/jats:p>","DOI":"10.1093\/nar\/gkab853","type":"journal-article","created":{"date-parts":[[2021,9,14]],"date-time":"2021-09-14T11:19:43Z","timestamp":1631618383000},"page":"D1408-D1416","source":"Crossref","is-referenced-by-count":63,"title":["VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases"],"prefix":"10.1093","volume":"50","author":[{"given":"Dandan","family":"Huang","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China"},{"name":"Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6527-9802","authenticated-orcid":false,"given":"Yao","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China"},{"name":"Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China"}]},{"given":"Xianfu","family":"Yi","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China"}]},{"given":"Xutong","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China"},{"name":"Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China"}]},{"given":"Jianhua","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China"},{"name":"Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China"}]},{"given":"Hongcheng","family":"Yao","sequence":"additional","affiliation":[{"name":"Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China"}]},{"given":"Pak Chung","family":"Sham","sequence":"additional","affiliation":[{"name":"Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China"}]},{"given":"Jihui","family":"Hao","sequence":"additional","affiliation":[{"name":"Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China"}]},{"given":"Kexin","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3598-3679","authenticated-orcid":false,"given":"Mulin Jun","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China"},{"name":"Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China"},{"name":"Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China"}]}],"member":"286","published-online":{"date-parts":[[2021,9,27]]},"reference":[{"key":"2022010507350420100_B1","doi-asserted-by":"crossref","first-page":"5900","DOI":"10.1038\/s41467-020-19653-5","article-title":"15 years of genome-wide association studies and no signs of slowing down","volume":"11","author":"Loos","year":"2020","journal-title":"Nat. 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