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Linkage Disequilibrium
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SNiPA - a tool for annotating and browsing genetic variants

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.

Variant Browser
Explore the functional annotations of variants.
Association Maps
Map trait associations from NHGRI's GWAS Catalog to karyograms.
Variant Annotation
Access detailed variant annotations.
Block Annotation
Summarize variant annotations within LD blocks or chromosomal regions.
Regional Association Plot
Visualize and annotate the results of genetic association studies.
Linkage Disequilibrium Plot
Combine LD data and annotations in an interactive plot.
Proxy Search
Find variants that are linked to other variants by LD.
Pairwise Linkage Disequilibrium
Determine the pairwise LD for two or more variants.
See how to use SNiPA and its interactive features.

Current release

SNiPA v3.4 (released November 13th, 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.

If you have feedback, problems or questions regarding SNiPA, feel free to contact us.
Some of SNiPA's features only work on modern browsers. SNiPA was successfully tested on Microsoft Edge ≥ 86, Firefox ≥ 82, Safari ≥ 13, and Chrome ≥ 86.

Please note that SNiPA stores a temporary cookie containing a session ID on your computer. This session ID is needed for several SNiPA tools, such as the SNiPA clipboard. The cookie will be deleted from your computer when you close your browser. Any data that you may upload during your site visit will be stored in temporary files on our server. These files are inaccessible to other users and will be deleted irreversibly within 24 hours.