Non-random association of phenotypes with ENCODE cell types strengthens the argument that at least some of the GWAS lead SNPs are functional or extremely close to functional variants. Each of the associations between a lead SNP and an ENCODE annotation remains a credible hypothesis of a particular functional element class or cell type to explore with future experiments. Supplementary Tables M1, M2 and M3 list all 14,885 pairwise associations across the ENCODE annotations. The accompanying papers have a more detailed examination of common variants with other regulatory information 76.
