For the trans- association, we selected a subset of phase II HapMap SNPs that have a higher probability of being functional than randomly selected SNPs of the genome. We selected SNPs of four categories: i) All SNPs with significant cis- associations, ii) All nsSNPs (rs numbers from Ensembl v41, genotypes extracted from HapMap v21), iii) All splice SNPs (rs numbers from Ensembl v41, genotypes extracted from HapMap v21), and iv) microRNA SNPs (as annotated in miRBase; genotypes from HapMap v21). Together these categories comprised a set of approximately 29,000 SNPs with MAF > 5% in each of the four populations.
