Figure 5 shows how the additive and dominance parameter estimates at the hit SNPs vary with LD, for simulations where the causal SNP is dominant. As predicted by theory, the dominance parameter tends toward the null value of 0 at a faster rate than does the additive parameter. Note that these plots show data covering the entire range of causal allele frequencies in the ENCODE regions, unlike the theoretical curves (Figs. 2–4), which are only for two specific values.
