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/.