Evolutionary signatures of common human cis-regulatory haplotypes

Variation in gene expression may give rise to a significant fraction of inter-individual phenotypic variation. Studies searching for the underlying genetic controls for such variation have been conducted in model organisms and humans in recent years. In our previous effort of assessing conserved underlying haplotype patterns across ethnic populations, we constructed common haplotypes using SNPs having conserved linkage disequilibrium (LD) across ethnic populations. These common haplotypes cluster into a simple evolutionary structure based on their frequencies, defining only up to three conserved clusters termed 'haplotype frameworks'. One intriguing preliminary finding was that a significant portion of reported variants strongly associated with cis-regulation tags these globally conserved haplotype frameworks. Here we expand the investigation by collecting genes showing stringently determined cis-association between genotypes and expression phenotypes from major studies. We conducted phylogenetic analysis of current major haplotypes along with the corresponding haplotypes derived from chimpanzee reference sequences. Our analysis reveals that, for the vast majority of such cis-regulatory genes, the tagging SNPs showing the strongest association also tag the haplotype lineages directly separated from ancestry, inferred from either chimpanzee reference sequences or the allele frequency-derived haplotype frameworks, suggesting that the differentially expressed phenotypes were evolved relatively early in human history. Such evolutionary signatures provide keys for a more effective identification of globally-conserved candidate regulatory haplotypes across human genes in future epidemiologic and pharmacogenetic studies.