Figure 2. Signal plots presenting 99% credible sets of SNPs at the JAZF1 and SLC30A8 loci.
The credible sets were constructed on the basis of: (i) the meta-analysis of European ancestry GWAS only (12,171 cases and 56,862 controls); and (ii) the trans-ethnic meta-analysis of European, East Asian, South Asian, and Mexican and Mexican American ancestry GWAS (26,488 cases and 83,964 controls). In each panel, each point represents a SNP passing quality control in the MANTRA analysis, plotted with their Bayes’ factor (on a log10 scale) as a function of genomic position (NCBI Build 36). The lead SNP is represented by the purple symbol. The colour coding of all other SNPs indicates LD with the lead SNP (estimated by Phase II HapMap CEU r2 for the European ancestry meta-analysis and CHB+JPT for the trans-ethnic meta-analysis to highlight differences in structure between ancestry groups): red r2≥0.8; gold 0.6≤r2<0.8; green 0.4≤r2<0.6; cyan 0.2≤r2<0.4; blue r2<0.2; grey r2 unknown. The shape of the plotting symbol corresponds to the annotation of the SNP: upward triangle for framestop or splice; downward triangle for non-synonymous; square for synonymous or UTR; and circle for intronic or non-coding. Recombination rates are estimated from Phase II HapMap and gene annotations are taken from the University of California Santa Cruz genome browser. The genomic region covered by the 99% credible set is highlighted in grey.