title: 3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes.
abstract: The vast noncoding portion of the human genome harbors a rich array of functional elements and disease-causing regulatory variants. Recent high-throughput chromosome conformation capture studies have outlined the principles of these elements interacting and regulating the expression of distal target genes through three-dimensional (3D) chromatin looping. Here we present 3DSNP, an integrated database for annotating human noncoding variants by exploring their roles in the distal interactions between genes and regulatory elements. 3DSNP integrates 3D chromatin interactions, local chromatin signatures in different cell types and linkage disequilibrium (LD) information from the 1000 Genomes Project. 3DSNP provides informative visualization tools to display the integrated local and 3D chromatin signatures and the genetic associations among variants. Data from different functional categories are integrated in a scoring system that quantitatively measures the functionality of SNPs to help select important variants from a large pool. 3DSNP is a valuable resource for the annotation of human noncoding genome sequence and investigating the impact of noncoding variants on clinical phenotypes. The 3DSNP database is available at http://biotech.bmi.ac.cn/3dsnp/.
authors: Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China.
authors: Yiming
authors: Y
authors: Lu
authors: Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China.
authors: Cheng
authors: C
authors: Quan
authors: Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China chb-1012@163.com.
authors: Hebing
authors: H
authors: Chen
authors: Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China boxiaoc@163.com.
authors: Xiaochen
authors: X
authors: Bo
authors: Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China zhangcglab@gmail.com.
authors: Chenggang
authors: C
authors: Zhang
mesh_terms: D002843:Chromatin; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D004843:Epistasis, Genetic; D005786:Gene Expression Regulation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D020506:Untranslated Regions; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D002843:Chromatin; D020506:Untranslated Regions