Optional filtering of SNPs based on functional annotations obtained in step 2 of SNP2GENE (i.e., CADD score, RegulomeDB score, 15-core chromatin state) can be performed for positional, eQTL and chromatin interaction mappings separately. When any of these filters is activated, candidate SNPs are filtered primary to gene mapping. Note that this filtering of SNPs based on functional annotations for a certain mapping does not affect other mappings, e.g., when SNPs are filtered by CADD score in positional mapping but not in eQTL mapping, SNPs are filtered prior to positional mapping but eQTL mapping uses the original set of candidate SNPs.
