We can use the results from Table 1 to interpret the results presented in Table 2. First, we note that the mean effect size (expressed as an odds ratio) across the studies that report a significant effect is 1.35. Second, all of the variants tested, whether significant or not, are common; none have an MAF less than 10%, and the mean is 38% (column headed MAF in Table 2). This means that the results of GWAS are relevant (recall that GWAS interrogates common variants). Virtually all of the candidate variants should be detectable by the published GWAS, particularly if imputation is used to obtain data from markers not present on the arrays (Howie et al., 2009) (Figure 1). The fact that the candidate variants do not occur in Table 1 suggests that the results in Table 2 are false positives (recall that the largest published GWAS has greater than 80% power to detect an odds ratio greater than 1.2).
