Figure 3.

Empirical rejection rates vs. R-squared between the proximal and distal marker, by proportion of variance explained by the QTL (left and right panels) and sample size (curves). The simulation setting here was the same as that in Figure 2: a single QTL ($z_i$) had an additive effect that explained either 1% (left) or 0.5% (right) of the phenotypic variance. The empirical model considered two SNPs with no causal effect. One of them ($x_{1i}$) was adjacent to the QTL and the other one ($x_{2i}$) was placed at increasing distance from the pair ($x_{1i},z_i$). Rejection of the null hypothesis (no interaction between $x_{1i}$ and $x_{2i})$was conducted at a 0.05 significance level. Empirical rejection rates above 0.05 are indicative of phantom epistasis.