Figure 2
From: Exhaustive search for epistatic effects on the human methylome
Example of a main effect of a SNP causing a spurious significant interaction effect between two other SNPs. Data is shown for cg00022866 from the discovery sample. (a) rs11231741 shows a strong main effect (p = 4.5 × 10−112). This causes a spurious significant interaction (b p = 3.3 × 10−18) because rs11231741 is in LD with both interacting SNPs (rs11231740: r 2 = 0.55; rs2236648: r 2 = 0.25). Of note, the two interacting SNPs show low LD only (r 2 = 0.024). Panel (c) depicts the dependencies between the 9 SNP-groups build from rs11231740 and rs2236648 and the 3 SNP-groups from rs11231741 (color-coded in black, red and green; a jitter has been added to the data): the 9 SNP-groups of the interacting SNPs mimic the three SNP-groups of the main effect, with 5 of the 9 groups mainly corresponding to the homozygous common allele carrier (black), 3 of the 9 groups mainly corresponding to the heterozygous group (red) and 1 group mainly corresponding to the homozygous rare allele carrier (green). Panel (d) shows the same data as in (b), but now with color-coding of the three SNP-groups from rs11231741.
