of main interest in the eQTL analysis. The p-value of the SNP effect in each eQTL model was calculated using a likelihood ratio (LR) test with the D = −2*log(LR) as the test statistic, which can be approximated by a Chi-square distribution with one degree of freedom. The p-values were adjusted for multiple testing by FDR correction [58]. In the replication study the batch effect was omitted from the model due to change of Illumina platform from 96-array format to 12-array format with no apparent batch differences present. For the eQTL analysis results were considered to be replicating in the replication study if the fixed effect of interest (β) had a p-value<0.05 and consistent direction of the effect. If quality control criteria for SNP genotyping of particular SNPs were not met in the replication study, a proxy - SNP were instead reported with better genotyping quality.
