We have reported that a large fraction of genes exhibiting cis- associations at the 0.001 permutation threshold are shared (about 37%) in at least two populations (Table 2 and 19). This comparison refers to the across-population association of the same gene and in most cases the same SNPs. The gold standard for association replication requires the same SNP to be associated with the same phenotype, and the allelic effects to be in the same direction across multiple independent populations. We compared the allelic directions of SNP-gene associations shared in all pairs of populations. In 95-97% of the shared associations, the direction of the allelic effect was the same across populations (Figure 3), and the discordant 3-5% is of the same order as the FDR. This further corroborates that the associations we observed represent real genetic effects on gene expression.
