We assessed (a) whether MAF is correlated with individual European admixture, and (b) the impact of European admixture in association. We only included EA and HS for this analysis since these populations were polymorphic for this SNP. Indeed, MAF increased for the rs2476601 risk allele (A) as the proportion of European Admixture increased ( Figure 2 ). Next, individuals were grouped by European admixture proportion and allelic association was performed for each group. For individuals with low proportions of European admixture (below 40%; 157 cases and 132 controls) and those with moderate proportions of European admixture (40–90%; 662 cases and 380 controls) rs2476601 was not associated with SLE, Plow = 0.60 and Pmoderate = 0.10 respectively. For individuals with the highest proportion of European admixture (>90%; 3648 cases and 3450 controls) this SNP was significantly associated with SLE (Phigh = 4.84×10−9). Similar results were found for rs1217414 (Plow = 0.40, Pmoderate = 0.78, Phigh = 0.007).
