3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database. Issue Volume 50:Issue D1(2022) (1st November 2021)

• Record Type: Journal Article
• Authors: Quan, Cheng; Ping, Jie; Lu, Hao; Zhou, Gangqiao; Lu, Yiming
• Is Part Of: Nucleic acids research. Volume 50:Issue D1(2022)
• Page Start: D950
• Page End: D955
• Publication Date: 2021-11-01
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkab1008
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: 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/ .