As a verification of the heuristic system, we compared the enrichment of SNVs associated with a GWAS (Supplemental Table S1; Hindorff et al. 2009). In all cases, SNVs in perfect linkage with GWAS lead SNVs are significantly enriched for the heuristic categories, and the level of this enrichment increases in tandem with higher-confidence categories. Detailed analysis of the application of RegulomeDB to GWAS and the enrichment of GWAS SNVs in functional regions is available as an additional ENCODE companion paper (Schaub et al. 2012).
