Supplementary Figure 8: Distribution of Nica et. al ’s rank statistic. The statistic is evenly distributed within [0,1] when the LD between the causal variants is negligable, but is increasingly biased towards 1 as the LD increases. Columns are divided by the r 2 between distinct causal variants, with r 2 = 1 indicating a shared causal variant. The top row shows the optimal result that could be obtained if conditioning on the true causal variant were possible, the bottom row shows the effect of conditioning on the most associated SNP is to reduce the degree of skew. Results are shown for a complete genotyping scenario, with a sample size of 2000 and a relative risk of 1.3. Similar effects are seen under tagging or complete genotyping approaches, but the skew towards 1 occurs more rapidly with larger samples and effect sizes. 36 [0,0.1] (0.1,0.5] (0.5,0.8] [0.8,1) 1 0 10 20 30 0 10 20 30 True causal SNPs Most associated SNPs 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0 Scaled rank density