Interpreting the results presented in Table 1 requires an understanding of what GWAS detects. GWAS interrogates common variation in the genome, usually variants with frequencies greater than 5%, and typically requires a genome-wide significance threshold of 5 × 10−8 (Pe’er et al., 2008) (this threshold depends on a number of factors, including the number of variants tested, also listed in Table 1). For the diallelic SNPs that are genotyped on GWAS arrays, allele frequencies are usually reported as the frequency of the least common allele (which will always be <0.5). This is the minor allele frequency (MAF).
