Fig. 2

Quantile-quantile (QQ) and distance plots. a QQ plots for three different analysis categories. The red line indicates local meQTL effects (SNP and methylation site < 1 Mb apart), the light blue line indicates distant meQTL effects where SNP and site are on the same chromosome (SNP and methylation site >1 Mb apart), while the dark blue line indicates cross-chromosome meQTL effects. The thin gray diagonal line indicates the expectation under the null hypothesis. b Distance plots for meQTL effects, where the x-axis shows the distance between SNP and methylation site and the y-axis shows the negative logarithm (base 10) of the p values. Note the y-axis scale of the plots is identical to the QQ plots, allowing direct comparison. In the left distance plot, the distribution of all meQTL effects around methylation sites indicates that most effects occurred within a distance of 500 kb. The central distance plot shows just the most significant SNP per methylation site, indicating that this is typically close. The right distance plot displays only the closest SNP with FDR < 0.01 to each site. The narrow spike indicates that the phenomenon is highly localized. The difference between the left and right distance plots is primarily due to linkage disequilibrium between SNPs