Allelic heterogeneity of local regulatory variation. (A) Associated SNPs detected at different FDR thresholds from GWA of gene expression were grouped to local and distant regulatory regions. At FDR < 0.2, for example, 1238 genes (67.4%) were associated with a single distant region (1 dist), 82 genes (4.5%) were associated with multiple distant regions (>1 dist), 444 genes (24.2%) were only locally associated (local), and an additional 74 genes (4.0%) were associated with both local and distant regions (local & dist). (B) For associations detected at FDR < 0.2 from GWA of gene expression, the number of genes that have single eQTL within local regulatory region (local 1), multiple eQTL within local regulatory region (local >1), single eQTL within distant regulatory region (dist 1), and multiple eQTL within distant regulatory region (dist >1). Associated SNPs within a regulatory region were clustered at different LD thresholds. (C) Distribution of eQTL from local scan. Proportion of eQTL (the number of eQTL after clustering by r2 > 0.8/[the number of SNPs tested]) was plotted along 500-bp bins for 25 kb upstream and 25 kb downstream. Within genes, the positions were binned to five positional quantiles. (Gray bars) The proportion of associated SNPs before LD clustering. (s) Transcriptional start site; (e) transcriptional stop site. (D) The P-value distribution of the F-tests for model comparison. Associated SNPs were clustered at different LD thresholds. (Dashed line) P-value of 0.05.
