snpXplorer: a web application to explore SNP-associations and annotate SNP-sets

Abstract

Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which involves advanced bioinformatic skills. We developed snpXplorer, an easy-to-use web-server application for exploring Single Nucleotide Polymorphisms (SNP) association statistics and to functionally annotate sets of SNPs. snpXplorer can superimpose association statistics from multiple studies, and displays regional information including SNP associations, structural variations, recombination rates, eQTL, linkage disequilibrium patterns, genes and gene-expressions per tissue. By overlaying multiple GWAS studies, snpXplorer can be used to compare levels of association across different traits, which may help the interpretation of variant consequences. Given a list of SNPs, snpXplorer can also be used to perform variant-to-gene mapping and gene-set enrichment analysis to identify molecular pathways that are overrepresented in the list of input SNPs. snpXplorer is freely available at https://snpxplorer.net. Source code, documentation, example files and tutorial videos are available within the Help section of snpXplorer and at https://github.com/TesiNicco/snpXplorer. Key points: O_LIsnpXplorer shows GWAS summary statistics, regional information and helps deciphering GWAS outcomes C_LIO_LIsnpXplorer interactively compares association levels of a genomic region across phenotypes C_LIO_LIsnpXplorer performs variant-to-gene mapping and gene-set enrichment analysis C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/377879v2_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@13a9ba5org.highwire.dtl.DTLVardef@c07b9aorg.highwire.dtl.DTLVardef@f2ce4forg.highwire.dtl.DTLVardef@c6d228_HPS_FORMAT_FIGEXP M_FIG C_FIG