Welcome to SNiPA!

SNiPA offers both functional annotations and linkage disequilibrium information for bi-allelic genomic variants (SNPs and SNVs). SNiPA combines LD data based on the 1000 Genomes Project with various annotation layers, such as gene annotations, phenotypic trait associations, and expression-/metabolic quantitative trait loci. See the documentation for all data sources integrated into SNiPA. For information on updates and new releases, see the Release Notes.

Current release

SNiPA v3.4 (released November 13^th, 2020)

Genome assembly: GRCh37.p13   Ensembl version: 87   1000 genomes: phase 3 version 5

SNiPA now incorporates two recent mQTL studies by Schlosser et al. (Nature Genetics, Feb 2020) and Lotta et al. (preprint, Jul 2020), as well as pQTLs in the context of SARS-CoV-2 from Pietzner et al. (preprint, Jul 2020). Additionally, over 4 million unique pooled and sex-specific associations from the Neale lab UK Biobank GWASs were integrated. Further updates include the most recent versions of GTEx for eQTL data as well as the GWAS Catalog, HGMD public and ClinVar, totalling to more than 940,000 genetic trait associations.

For further information, see the release notes or the documentation.

Did you use SNiPA for a publication? We would appreciate if you cite us:

Arnold M^‡, Raffler J^‡, Pfeufer A, Suhre K, and Kastenmüller, G. SNiPA: an interactive, genetic variant-centered annotation browser. Bioinformatics first published online November 26, 2014 doi:10.1093/bioinformatics/btu779 OPEN ACCESS.
^‡These authors contributed equally.