We identified three regions where the haplotype sequence had a significant (p-value<0.001) effect on reporter activity (luminescence) in the same allelic direction as the expression measurements, including two promoters and one 3′UTR region (Figure 5 and Figure S12). No significant but discordant effects were observed. Variants near PRMT6, which encodes a protein-arginine methyltransferase and has been associated with HIV infection progression [38], scored highly in both the UW and UC eQTL analysis (Figure 5A). Resequencing of the PRMT6 promoter yielded two common haplotypes defined by two perfectly correlated SNPs located 406 and 150 bp upstream from the TSS. The minor haplotype (40% frequency) correlated with a strong additive decrease in PRMT6 liver expression (t-test p-value = 6.4×10−14 for UW), and relative to the major haplotype, we found a concomitant decrease in luminescence for reporter constructs harboring the minor haplotype (p-value = 0.0002). A similar result was obtained for promoter haplotypes of the LDHC (lactate dehydrogenase C) gene in which six common variants defined 7 common haplotypes, five of which were successfully cloned and tested. The strongest expression correlation was observed
