Cis-eQTL mapping was performed in each cohort using a pipeline described previously5. In brief, the pipeline takes a window of 1 Mb upstream and 1 Mb downstream around each SNP to select genes or expression probes to test, based on the center position of the gene or probe. The associations between these SNP–gene combinations are calculated using Spearman correlation. Next, every cohort performed 10 permutations. In each permutation, the links between genotype and expression identifiers were shuffled prior to re-calculating all associations. Both the non-permuted results and each round of permuted results were meta-analyzed across cohorts.
