Comparison of the five tests when applied to meQTLs data. The P-values of AdaJoint, ARTP and Min-p were calculated from 109 replicates of permutation. For each methylation trait, we tested its association with the SNPs within 100 kb from the target CpG site. The blue solid circles represent the CpG sites where AdaJoint identified a single-marker model as the best risk model. The red solid circles and triangles represent the CpG sites where AdaJoint identified a best risk model with multiple SNPs. The red solid triangles represent the seven CpG sites where AdaJoint identified a best model with multiple SNPs and had the P-value less than 1.0 × 10−5. More results about these seven CpG sites are given in Table 3.