Figure 4—figure supplement 3. | Passive and active DNA methylation and the interplay with genetic variation in gene regulation

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Passive and active DNA methylation and the interplay with genetic variation in gene regulation

Figure 4—figure supplement 3.

Affiliation details

University of Geneva Medical School, Switzerland; Institute of Genetics and Genomics in Geneva, Switzerland; Swiss Institute of Bioinformatics, Switzerland; Stanford University, United States
Figure 4—figure supplement 3.
Download figureOpen in new tabFigure 4—figure supplement 3. Interactions between SNPs and transcription factor levels on DNA methylation.

(A) We tested whether genetic variants that could potentially alter TF binding would interact with TF abundance (transcription level) on their effect on DNA methylation levels. To do so we took the top mQTL SNPs that fell in TF peaks and whose associated methylation site correlated significantly with the TF expression level of that peak (10% FDR for both types of associations), and required that the SNP and the TF abundance were not correlated and that the SNP had at least four minor allele homozygotes (N = 114). (B) We find an enrichment of low p values for interactions between genetic variants and TF abundance on DNA methylation levels, with π1 estimating 15% of true positives. (C) Plotted is the top interaction with p=1×10−4 involving the TF c-Jun in T-cells. The SNP falls in the binding peak of c-Jun. The methylation site and the SNP are 172 bp away from each other and both fall in an intron of gene SLC9A9.

DOI: http://dx.doi.org/10.7554/eLife.00523.022