Small P-value GWAS SNPs were considered in the previous pipeline if they occur within a specified candidate gene, but for those in the remainder of the genome we provide additional means of selection based on function and evolutionary conservation (Figure 2A). In providing this screen we consider not only all the GWAS SNPs that were found to have small P-values, but the much larger set of SNPs in dbSNP that meet two criteria: (i) they are within a user-specified distance from a small P-value GWAS SNP; and (ii) they are known to be in high LD with a small P-value GWAS SNP. From this large pool we screen SNPs based on functional predictions and apply MAF filters. Finally, we eliminate redundant SNPs based on a user-defined LD threshold.
