Overview of regulatory variant discovery workflow. The analysis workflow takes as input a list of SNPs identified in genome wide association studies, diverse high-throughput sequencing data related to the delineation of cis-regulatory sequences, and position weight matrices (PWMs). The input SNP lists are extended to SNPs in high linkage disequilibrium (LD). Functionality of each SNP is evaluated through the three criteria (regulatory potential, TF binding affinity and binding evidence). The output is a set of candidate variants that display characteristics consistent with a cis-regulatory role in the disease process.