To perform enhancer enrichment analysis on sets of variants, tables of common array designs were obtained from the UCSC Table Browser (34) and lists were constructed of 1000 Genomes SNPs segregating in each of the three pilot populations, as well as all SNPs in the database. Then, a background frequency of coverage was calculated for variants annotated as overlapping a strong enhancer state in each cell type. When a user submits a query list of variants, the coverage of strong enhancers in each cell type is calculated. If the coverage exceeds that of the background set selected by the user, a binomial test is performed, and enrichment is reported if it passes an uncorrected significance threshold of 0.05.
