We note that the RORA locus is 6.4 Mb away from a known asthma variant (rs744910 near SMAD3), but these two loci are independent, because there is low linkage disequilibrium between these two variants (pairwise linkage disequilibrium, r2 = 0.01 in HapMap CEU panel) and because the association estimates for these two variants are virtually unchanged when conditioned on each other (Table S3). Here, SMAD3 is linked to asthma.