It is especially valuable for prioritizing candidate SNPs identified by the GWAS, or novel or rare variants discovered from the direct human genome sequencing. Promoter regions were used as an example of regulatory regions to illustrate the procedures involved. In this study, we proposed a three-step bioinformatics approach to identify functional SNPs within the regulatory regions following GWAS. It has been reported that E2F1 can serve as both positive and negative regulator on their target genes (Crowe et al., 2001