Intriguingly, 13 of the 88 eQTL SNPs in whole blood were observed to have opposite effects on expression levels in whole blood and lymphoblastoid cell lines. Dimas et al. [9] compared gene expression variation in fibroblasts, lymphoblastoid cell lines, and T cells and reported that the same directional effect in each cell type was observed for eQTLs shared between multiple cell types. However, 2 recently published studies reported that some eQTL SNPs have opposite allelic effects on gene expression in the liver, adipose tissue, skeletal muscle [10], or in B cells and monocytes [11]. Our findings also suggest the possibility that some SNPs may exert opposite effects on gene expression in different cell types. However, an alternative explanation may be that the eQTL SNPs identified may function to alter the splicing of the mRNA. Since the gene expression microarray platform used in the previous eQTL study examining LCL expression levels in Japanese subjects was different from ours, the different probes may have detected different splicing variants, resulting in seemingly opposite allelic effects. A comparison using the same platform would be necessary to uncover cell-specific effects on expression levels.
