Analyses of rs9478500 conditioning on rs1799971 and vice versa using GCTA-COJO37,38 showed only modest decrements in statistical significance for each variant compared to their unconditional models: rs9478500 (p = 2.56 × 10–9 for the gSEM analysis vs. p = 2.04 × 10–7 for the conditional analysis); rs1799971 (p = 1.94 × 10–6 for the gSEM analysis vs. p = 1.41 × 10–4 for the conditional analysis). These results suggest that these variants have largely independent associations. However, GCTA-COJO only accounts for LD in terms of r2, which is low between these variants among those of European ancestry (r2 = 0.035). In contrast, perfect D’ (1.0) between these variants indicates a strong dependency in the haplotype structure and a need to examine haplotypes.
