The current study showed that several of the SNPs affecting the expression levels of a gene in whole blood also influenced the expression levels of the same gene in lymphoblastoid cell lines. A recent study by Powell et al. [22] has shown that the genetic control mechanisms of gene expression in whole blood and lymphoblastoid cell lines are largely independent. Despite the evidence of low genetic correlation of regulatory variation averaged across the genome, our results suggest that a subset of eQTLs commonly affect expression levels in whole blood and lymphoblastoid cell lines. Conversely, our findings suggest that some of the whole blood eQTL SNPs do not regulate expression levels in lymphoblastoid cell lines. This is in line with a previous study that reported that 69–80% of the identified regulatory variants operated in a cell type-specific manner [9]. Compared to SNPs affecting only expression levels in whole blood, higher, although not statistically significant, proportion of SNPs affecting expression levels in both whole blood and lymphoblastoid cell lines were in LD with SNPs located on TFBSs and miRNA-binding sites. The finding suggests that these functional properties affect expression levels across multiple cell types.
