We also looked for a pattern in terms of which loci replicated. Logically, the largest replication indicator was discovery P-value, as stronger associations likely require a smaller sample size for replication than weaker ones. In GERA, loci with P≤1×10−9 replicated at a Bonferroni level at a rate of 76.5% (13/17) vs. 54.5% (12/22) for those with 5×10−8≤P<1×10−9; all of the ICBP SNPs with P≤1×10−9 replicated at a Bonferroni level in GERA+UKB; however, the pattern was not seen in the GERA and ICBP meta-analysis with 57.1% (4/7) with P≤1×10−9 vs. 62.1% (18/29) with 5×10−8≤P<1×10−9 although numbers were small. Perhaps also of note, the two SNPs in GERA with MAF<0.001 failed to replicate in UKB (P>0.05).
