The rapid development of single-molecule sequencing and single-cell ATAC (assay for transposase accessible chromatin) sequencing (scATAC-seq) techniques presents new challenges and opportunities for the annotation of human noncoding variants. Here, we updated 3DSNP, a comprehensive database for human noncoding variants annotation, to expand its applications to structural variation (SV) and to zoom variants annotation into the single-cell resolution. The updates of 3DSNP include:
(i) annotation of 107,590 SVs from a full spectrum of functions, especially their potential effects on three-dimensional chromatin structures,
(ii) evaluation of the chromatin accessibility surrounding the variants in 126 cell types/subtypes in 15 fetal tissues and 54 cell types/subtypes in 25 adult tissues using scATAC-seq data and
(iii) expansion of Hi-C data to 49 human cell types.
In summary, it is a significant and comprehensive improvement over the previous version.
- Quan C, Ping J, Lu H, Zhou G, Lu Y, 3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database, Nucleic Acids Research 2021, gkab1008 https://doi.org/10.1093/nar/gkab1008 PubMed
The old version: