Results of the linear mixed-effects models on genome-wide linkage disequilibrium (LD, distance-corrected <i>r</i>² between pairs of SNPs) or the correlation of zygosity (Δ) of genic regions and (top) intergenic regions (bottom).

For each fixed effect, the model estimate (β) as well as the chi-square statistics (χ2) with the associated p value from type III Wald χ2 tests are given. For the correlation of zygosity, the results for Δ at 1000 bps distance are shown (see also S7 Fig). Only results for fixed effects are shown.