Furthermore, to investigate regulatory regions, we employ a two tiered approach to investigate cell type specific enrichment within DNase I sites using FORGE, which tests for enrichment of SNVs within DNase I sites in 123 cell types from the Epigenomics Roadmap Project and ENCODE71 (Supplementary Note). Validated sentinel SNVs from our study are analysed along with previously reported SNVs at the time of analysis and secondary signals (with P-value < 1×10-4) to evaluate the overall tissue specific enrichment of BP associated variants. In a second analysis we use FORGE (with no LD filter) to investigate directly our curated candidate regulatory SNVs for overlap with cell-specific DNase I signals.
