A threshold of P<5x10-8 is a valid threshold for genome-wide significance in GWAS analyses of common variants45. Our genotyping and imputation strategy resulted in testing of 27.6 million variants of which 21.6 million had MAF<5% and 18.2 million had MAF<1%. Although all of our 43 signals were common, had we adopted a stricter threshold for genome-wide significance, for example, P<1x10-8 (recommended in a recent report of significance thresholds in whole genome sequencing45), only two of our signals (rs10246303:A>T in the 3’ UTR of C1GALT1 on chromosome 7, and rs1698268:A>T near LINC00911 on chromosome 14) would not have reached significance. Thirty-nine of the 43 signals were additionally supported by statistically significant independent replication in stage 2 (P<0.05/43, Supplementary Table 3).
