Predicting Signatures of “Synthetic Associations” and “Natural Associations” from Empirical Patterns of Human Genetic Variation
Figure 1
Distance of synthetic and natural associations from the causal variant it is in greatest LD with.
Box plot of the distance between any associated SNP and causal variant it is in highest LD with, measured in r2, for (a) YRI and (b) CEU in four scenarios: 2 common causal variants with a GRR of 1.5 (dark blue), 2 common causal variants with an unrealistic GRR of 3 (light blue), 5 and 9 rare causal variants with a GRR of 3 (red and gold respectively). Distances vary greatly between the different disease loci (x-axis) as well as between populations, but in all regions the median (line within each box) is larger for rare causal variants than for common causal variants of lower effect size. Increasing the effect size can result in higher association distance as is observed most notably in region #5.