When we compare the sets of genes exhibiting cis- associations identified using the phase I HapMap 19 to those identified using the phase II HapMap data, we observe that the phase I HapMap captured 79%-87% (depending on the population) of the genes detected with phase II. Only in YRI is there is a substantial gain in numbers of cis- associated genes (Figure S5 and Figure 1A). This is due to the fact that in the other three populations, linkage disequilibrium (LD) decays much more slowly, so that instead of capturing the vast majority of common haplotype diversity, in the YRI the phase II captures additional functional genetic variation relative to phase I HapMap.
