snpXplorer

snpXplorer facilitates exploration of single nucleotide polymorphism (SNP) associations from genome-wide association studies (GWAS) and integrates multi-source genomic annotations to support functional interpretation, variant-to-gene mapping, and gene-set enrichment analysis.

Key Features:

• Integration and Comparison of GWAS Data: Superimposes association statistics from multiple GWAS to compare SNP associations across traits and studies.
• Functional Annotation of SNPs: Provides regional annotations including structural variations, recombination rates, expression quantitative trait loci (eQTL), linkage disequilibrium patterns, and gene expression across tissues.
• Variant-to-Gene Mapping: Maps input lists of SNPs to candidate genes to associate variants with genes.
• Gene-Set Enrichment Analysis: Performs gene-set enrichment analysis to identify molecular pathways overrepresented among genes linked to input SNPs.

Scientific Applications:

• Genetic Association Studies: Integrates multiple GWAS and functional annotations to identify significant genetic variants and interpret their functional roles in human phenotypes.
• Cross-Trait Comparison: Compares SNP associations across traits to aid interpretation of genotype–phenotype relationships.

Methodology:

Computational steps explicitly include overlaying GWAS association statistics, functional annotation of SNPs (structural variation, recombination rates, eQTL, linkage disequilibrium, gene expression), and gene-set enrichment analysis.