For a given set of lead SNPs from a GWAS or user-input SNPs, the overlap of SNPs with predicted enhancers in each reference epigenome is assessed. Users have four different options for defining enhancers, available in the option panel: using the 15-state core model, using the 25-state model incorporating imputed epigenomes, using H3K4me1 peaks and using H3K27ac peaks. The overlap with enhancers in each cell type is compared to two background models to assess enrichment: all 1000 Genomes variants with a frequency above 5% in any population and all independent GWAS catalog SNPs. The enrichment relative to these background frequencies is performed using a binomial test and uncorrected P-values are reported in an enrichment table underneath the haplotype views.
