Documentation for 3DSNP


3DSNP is an integrated database for annotating the regulatory function of human noncoding SNPs by exploring their 3D interactions with genes and other SNPs mediated by chromatin loops. The model of cis-acting DNA elements regulating gene expression through three dimensional interactions mediated by chromatin loops have been established recently, and SNPs were reported frequently located in these elements. 3DSNP collects currently available Hi-C datasets from different studies, consist of 75,362 intrachromosome chromatin loops in twelve human cell types. Two types of linkages were defined according to the spectrums of the loops: “Within Loop” or “Anchor-to-Anchor”. Allele frequencies were obtained for the SNPs in 1000 Genomes Phase 3 data, and pairwise LD was calculated for all pairs of SNPs in each continental population (EAS, AFR, AMR, ASN, EUR) within 200 kb. 3DSNP also integrated chromatin state segments, transcription factor binding sites and DNA accessibility from the Roadmap Epigenomics and ENCODE projects, DNA-binding motifs from TRANSFAC and JASPAR databases, eQTLs from the GTEx project and sequence conservation from UCSC Genome Browser. Network- and Circos-based visualization tools were developed for 3DSNP to display interacting SNPs, genes and elements along with important epigenetic marks. A comprehensive scoring system was also developed to score all SNPs based on their functionality in different aspects. 3DSNP provides an integrated database and visualization tools for discovering the regulatory roles of noncoding SNPs mediated by 3D genome topology.


To learn more about 3SNP, have a look at the Tutorials.

3DSNP for Developers

To access 3DSNP in a more powerful way, check out our API.


Click the FAQs for more information.


To cite 3DSNP, please refer to our publication here.