SNiPA: an interactive, genetic variant-centered annotation browser

Abstract

Motivation: Linking genes and functional information to genetic variants identified by association studies remains difficult. Resources containing extensive genomic annotations are available but often not fully utilized due to heterogeneous data formats. To enhance their accessibility, we integrated many annotation datasets into a user-friendly webserver.

Availability and implementation: http://www.snipa.org/

Contact: g.kastenmueller@helmholtz-muenchen.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

The SNiPA Variant Browser shows variants (top), genes (center) and regulatory regions (bottom). Top-level information is available in mouse-over tooltips for all plot elements as shown here for the query SNP rs174583. The example highlights the value of variant-centered accumulation of annotations: rs174583 is associated with the concentration of a lipid metabolite as well as with the expression levels of two genes encoding enzymes involved in lipid metabolism (FADS1/2) and the gene coding for LDL receptor, a major regulator of cholesterol homeostasis. Furthermore, the variant was linked to the response to lipid lowering drugs (statins), which target HMG-CoA reductase regulated by the LDL receptor