The genetic contribution to expression variation was evaluated by genome-wide association with expression of all 22,300 probes. Starting with a simple test of the correlation between each transcript abundance and each genotype, and filtering to retain only eSNPs with a minor allele frequency greater than 0.05, we observed 3,430 associations at P < 10−8. Further filtering of eSNPs to retain only autosomal associations with annotated genes, and imposing the additional stringency of P < 10−11 for putative trans associations between an eSNP on one chromosome and a probe on another chromosome, reduced this to 1,636 associations. 1,569 (96%) of these are intra-chromosomal linkages, the vast majority within 50 kb and hence cis-acting(Supplementary Fig. 5 online), and only 3 clearly in different chromosomal intervals. Facsimile associations were observed for 39 of the target genes represented by a second probe (37 cis, 2 trans). Reducing the dataset further to exclude linked associations within haplotype blocks leaves 346unique cis and 10 unique trans associations at the stringent genome-wide 5% significance level. These proportions are in good agreement with most other GWAS expression studies
