Examining the SOM of integrated ENCODE annotations (see above), we found 19 SOM map units showing significant enrichment for GWAS SNPs, including many SOM units previously associated with specific gene functions, such as the immune response regions. Thus, an appreciable proportion of SNPs identified in initial GWAS scans are either functional or lie within the length of an ENCODE annotation (~500 bp on average) and represent plausible candidates for the functional variant. Expanding the set of feasible functional SNPs to those in reasonable linkage disequilibrium, up to 71% of GWAS SNPs have a potential causative SNP overlapping a DNaseI site, and 31% of loci have a candidate SNP that overlaps a binding site occupied by a TF (see also refs 74,76).
