Of the 47,294 probes for which we collected expression data, we selected a set of 21,800 probes for analysis. We included in our analyses each probe that mapped to an Ensembl gene, but not to more than one Ensembl gene (Ensembl 49 NCBI Build 36), and we excluded probes mapping to the X or Y chromosome. The final set of 21,800 probes considered for association mapping corresponds to 18,226 unique autosomal Ensembl genes. We mapped known 1000 genomes common SNPs (MAF>5%) from CEU, CHB, JPT, YRI (August 2010) to all probes. We found that of the 21,800 probes we used in our analysis, 1401 (6.4% of tested probes) overlapped a known common SNP. There is the risk of a SNP-in-probe effect for these overlapping variants, inducing false positive eQTLs. We decided to not simply exclude these probes in an overly-conservative manner, but instead tested for possible enrichment among statistically significant eQTLs and compared the degree of replication across populations for those cis-eQTLs with probes to those cis-eQTLs without probes.
