snpXplorer

snpXplorer enables exploration and annotation of Single Nucleotide Polymorphisms (SNPs) from Genome-Wide Association Studies (GWAS) to contextualize association signals and identify implicated molecular pathways.

Key Features:

• Multiple GWAS integration: Superimposes association statistics from multiple GWAS studies to compare levels of genetic association across traits.
• Regional genomic annotation: Displays regional data including SNP associations, structural variations, recombination rates, linkage disequilibrium patterns, genes, and tissue-specific gene expression.
• eQTL incorporation: Integrates expression Quantitative Trait Loci (eQTL) information to link regulatory variants with gene expression across tissues.
• Variant-to-gene mapping: Maps input lists of SNPs to candidate genes to support downstream functional interpretation.
• Gene-set enrichment analysis: Performs gene-set enrichment to identify molecular pathways overrepresented among mapped genes.
• Data integration and visualization: Integrates and visualizes diverse genomic data sources to display complex genetic association landscapes.

Scientific Applications:

• GWAS interpretation: Contextualizes SNP association statistics within genomic regions to aid interpretation of genetic signals for human phenotypes.
• Cross-trait comparison: Enables comparison of association statistics across traits to identify shared genetic factors among phenotypes.
• Functional annotation and pathway discovery: Annotates SNP sets with functional data (e.g., eQTLs, gene expression) and identifies implicated biological pathways.

Methodology:

Integrates and visualizes diverse genomic data sources to process and display complex genetic association data.