{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T18:43:56Z","timestamp":1780598636071,"version":"3.54.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771397"],"award-info":[{"award-number":["31771397"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005090","name":"Beijing Nova Program","doi-asserted-by":"publisher","award":["20180059"],"award-info":[{"award-number":["20180059"]}],"id":[{"id":"10.13039\/501100005090","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFA0504301"],"award-info":[{"award-number":["2017YFA0504301"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chinese Key Project for Infectious Diseases","award":["2018ZX10732202"],"award-info":[{"award-number":["2018ZX10732202"]}]}],"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>The rapid development of single-molecule long-read sequencing (LRS) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) technologies presents both challenges and opportunities for the annotation of noncoding variants. Here, we updated 3DSNP, a comprehensive database for human noncoding variant annotation, to expand its applications to structural variation (SV) and to implement variant annotation down to single-cell resolution. The updates of 3DSNP include (i) annotation of 108 317 SVs from a full spectrum of functions, especially their potential effects on three-dimensional chromatin structures, (ii) evaluation of the accessible chromatin peaks flanking the variants across 126 cell types\/subtypes in 15 human fetal tissues and 54 cell types\/subtypes in 25 human adult tissues by integrating scATAC-seq data and (iii) expansion of Hi-C data to 49 human cell types. In summary, this version is a significant and comprehensive improvement over the previous version. The 3DSNP v2.0 database is freely available at https:\/\/omic.tech\/3dsnpv2\/.<\/jats:p>","DOI":"10.1093\/nar\/gkab1008","type":"journal-article","created":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T01:05:05Z","timestamp":1634087105000},"page":"D950-D955","source":"Crossref","is-referenced-by-count":58,"title":["3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database"],"prefix":"10.1093","volume":"50","author":[{"given":"Cheng","family":"Quan","sequence":"first","affiliation":[{"name":"Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Ping","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Lu","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4895-5063","authenticated-orcid":false,"given":"Gangqiao","family":"Zhou","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8005-2705","authenticated-orcid":false,"given":"Yiming","family":"Lu","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,1]]},"reference":[{"key":"2022010507311293800_B1","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.ymeth.2012.05.001","article-title":"Hi-C: a comprehensive technique to capture the conformation of genomes","volume":"58","author":"Belton","year":"2012","journal-title":"Methods"},{"key":"2022010507311293800_B2","doi-asserted-by":"crossref","first-page":"R22","DOI":"10.1186\/gb-2010-11-2-r22","article-title":"ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing","volume":"11","author":"Li","year":"2010","journal-title":"Genome Biol"},{"key":"2022010507311293800_B3","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":"2022010507311293800_B4","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/s41576-020-0236-x","article-title":"Long-read human genome sequencing and its applications","volume":"21","author":"Logsdon","year":"2020","journal-title":"Nat. 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