We anticipated that SNPs replicate better in the same ancestral group in which they showed their initial association signals. The GWAS meta-analysis was the main source of SNP selection and involved European subjects only, which likely explains why SNPs replicated relatively better in the European group. Although non–major histocompatibility complex (MHC) SNPs replicated in all ancestral groups, the SNPs in the MHC region did not: we observed a large 3.7-fold enrichment of values of P<.01 in European samples, but findings dissipated in non-European samples. This pattern seems consistent with the exceptionally large LD differences across ancestral groups in this region resulting from its evolutionary significance (eg, it harbors many genes affecting the immune response).
