Figure 3
From: Rare non-coding variants are associated with plasma lipid traits in a founder population
Rare variants on chromosome 19 are associated with LDL-C. (a) Reweighted GWAS. GWAS results were reweighted using the joint model presented in Fig. 2. Each point represents a region of the genome and its corresponding posterior probability of association (PPA) in a model with and without enrichments. Red points correspond to regions in the bottom, grey points in the middle, and black points in the top tertiles of gene density. The dotted red line represents regional PPA > 0.75 in the enriched model. (b) Boxplot of association between LDL-C (y-axis) and candidate LDLR expression level by variant rs17242388 (p = 3.89 × 10 −15 ) (x-axis). Black horizontal lines show medians and whiskers show the 25th and 75th percentiles. (c) Locus plot. The top panel shows the p-values of association with LDL-C for all variants discovered in the Hutterites regardless of allele frequency in Europeans (y-axis). Symbols correspond to the maximum allele frequency in Europeans, with closed circles representing REVs (see legend), and are colored based on their LD r 2 with the most associated variant in the region (rs557778817). The next three panels show tracks for the annotations selected in the fgwas joint model, annotations of known GWAS loci from NHGRI, and the estimated PPA of being causal for each variant in the reweighted fgwas. The bottom-most panel shows the genes in the region.
