Next, we examined how GWAS variants in DHSs were distributed with respect to transcription factor recognition sequences, defined using a scan for known motif models at a stringency of P < 10-4 (12). Of GWAS SNPs in DHSs, 93.2% (2,874) overlap a transcription factor recognition sequence. We partitioned GWAS variants into 10 disease/trait classes, and then determined the frequency of GWAS variants associated with a particular disease/trait class that localized within sites for transcription factors independently partitioned into the same classes based on gene ontology annotations (fig. S8) (12). This analysis revealed that common variants associated with specific diseases or trait classes were systematically enriched in the recognition sequences of transcription factors governing physiological processes relevant to the same classes.
