gwas-cataloglisted

# Integrating NHGRI-EBI GWAS Catalog with ENCODE Regulatory Data ## When to Use - User wants to intersect ENCODE regulatory elements with GWAS-associated variants - User asks about "GWAS", "genome-wide association", "disease variants", or "trait-associated SNPs" - User needs to find which GWAS hits overlap enhancers, promoters, or TF binding sites - User wants to prioritize GWAS loci by functional annotation from ENCODE data - Example queries: "find GWAS variants in my H3K27ac peaks", "which diabetes GWAS hits overlap pancreas enhancers?", "annotate GWAS loci with ENCODE regulatory marks" Connect genome-wide association study findings with ENCODE functional annotations to identify which regulatory elements harbor disease-associated variants and prioritize causal mechanisms for non-coding GWAS hits. ## Scientific Rationale **The question**: "Which of the disease-associated variants from GWAS fall within active regulatory elements, and what can ENCODE tell us about their functional impact?" The GWAS Catalog (maintained by NHGRI-EBI) contains over 500,000 variant-trait associations from 6,000+ publications. The central challenge of post-GWAS analysis is that >90% of these associations point to non-coding regions of the genome. ENCODE provides the essential functional annotation layer: if a GWAS variant falls within an active enhancer in disease-relevant tissue, that enhancer becomes a candidate causal mechanism. This was first demonstrated systematically by Maurano et al.