We tested this as the explanation for the capacity of recombination to enhance associations by directly evaluating the mean and the variance of the association between rare and common variants in a simplified simulation. We considered two regions separated by a specified recombination rate. We calculated the average pairwise association between rare and common variants and also the variance of the pairwise LD between rare and common variants in each simulation, and evaluated both these parameters as a function of recombination. We found that although the mean is nonincreasing, the variance first increases then decreases (Figure 4), suggesting that increases in recombination can “widen” the distribution of LD among sites sufficiently to increase the density in the tail and thereby create stronger synthetic associations.
