Supplementary Figure 5: Characteristics of index variants for association signals achieving locus-wide significance for T2D susceptibility across fine-mapping regions.

Each association signal was represented by an index variant in the GCTA-COJO joint regression model on the basis of (i) summary statistics from the meta-analysis of Metabochip studies in 27,206 cases and 57,574 controls of European ancestry and (ii) reference genotype data from GoDARTS (3,298 cases and 3,708 controls of European ancestry from the UK) to approximate LD across fine-mapping regions. Each variant is plotted according to risk allele frequency on the x axis and allelic log(OR) on the y axis (with error bars representing the corresponding standard error).