Fig. 2

Manhattan and quantile–quantile plot (QQ-plot) of the discovery and replication genome-wide meta-analysis. The upper corner represents the QQ-plot. Expected −log₁₀ p-values under the null hypothesis are represented in the x axis, while observed −log₁₀ p-values are represented in the y axis. Observed p-values were obtained according to the suitable replication dataset used (as shown in Fig. 1) and were depicted using different colors. HapMap variants were meta-analyzed using the trans-ethnic summary statistics from the DIAGRAM study and our meta-analysis based on the Genetic Epidemiology Research on Aging (GERA) cohort and the northwestern NuGENE project, and that resulted in novel associations depicted in magenta. The rest of non-HapMap variants meta-analyzed using the full 70KforT2D cohort are represented in gray, and the fraction of novel GWAS-significant variants is highlighted in light blue. Coding low-frequency variants meta-analyzed using the 70KforT2D and the T2D Portal data that resulted in novel GWAS-significant associations are depicted in green. The shaded area of the QQ-plot indicates the 95% confidence interval under the null and a density function of the distribution of the p-values was plotted using a dashed line. The λ is a measure of the genomic inflation and corresponds to the observed median χ2 test statistic divided by the median expected χ² test statistic under the null hypothesis. The Manhattan plot, representing the −log₁₀ p-values, was colored as explained in the QQ-plot. All known GWAS-significant associated variants within known T2D genes are also depicted in red. X chromosome results for females (F), males (M), and all individuals (A) are also included