Because the eQTL mapping and lymphocyte count GWAS used different genotyping platforms, we allowed for a proxy SNP to replace the paired (eQTL) SNP if it was not included in the GWAS. To do so, we used SNAP (http://www.broadinstitute.org/mpg/snap/; 83), a web-based tool for identifying proxy SNPs, to generate a list of all SNPs in LD (at an r2 ≥ 0.5) with any of our eQTLs (r2 was based on HapMap LD, although results using 1000 genomes-based LD were broadly equivalent; data not shown). We chose the proxy SNPs with the highest LD to the eQTL SNP; if several proxy SNPs shared the same level of LD, we chose one at random to represent the eQTL SNP (see Supplementary Material, Fig. S7A for distribution of r2 values for proxy SNPs chosen).
