In order to detect cis-eQTLs, analysis was confined to those probe-SNP combinations for which the distance from the probe transcript midpoint to SNP genomic location was ≤250 kb. For trans-eQTLs, analysis was confined to those probe-SNP combinations for which the distance from probe transcript midpoint to SNP genomic location was ≥5 Mb (to exclude the possibility of accidentally detecting cis-eQTLs due to long ranging linkage disequilibrium). Additionally, for the trans-eQTL analysis the effects of the significant cis-eQTLs were removed from the expression data by keeping the residual expression after linear regression.
