Quantitative mRNA expression analysis in this study and previous studies have demonstrated that minor alleles of variants in the adjacent CHRNA5 promoter region and/or 5′distal promoter region increase CHRNA5 mRNA levels in post-mortem brain tissues and in lung tissue [19]–[21]. However, Doyle et al conducted a functional study that incorporated an 852 bp portion of the 5′ distal region of the CHRNA5 promoter and showed strongly repressed transcription in cells with heterologous promoter constructs, compared to control vector [25]. No significant difference of the relative promoter activities was detected between the all-minor-allele haplotype construct and the all-major-allele haplotype construct [25]. The contradictory findings between the in vitro study and ex vivo study maybe explained by exclusion of the regions of the CHRNA5 gene and adjacent promoter from the constructs used in Doyle et al study. Another possibility could be the tissue-specific nature of CHRNA5 RNA expression. For example, we observed that the genetic effects on CHRNA5 total mRNA expression in lymphoblastoid cells of European ancestry are in the opposite direction to that observed in human brains. Studies with promoter haplotypes,
