Fig. 4: Detection and examples of trimodal QTLs.
From: Genetic coupling of enhancer activity and connectivity in gene expression control
A Strategy for detecting trimodal QTLs using GUESS. Regions within 5 kb of ATAC-seq peaks and CHi-C DpnII bait fragments were identified, and all genotyped variants were queried within these regions. Created in BioRender: https://BioRender.com/f51r706. B Overview of the significant findings from the GUESS analysis. Created in BioRender: https://BioRender.com/w52b348. C Number of trimodal QTLs at 5% FDR that best explained the observed phenotypes in each window. D, E Examples of GUESS loci where the best model (combination of genetic variants with the largest marginal likelihood score) contained a single trimodal QTL (also significant at 5% FDR) that was associated with chromosomal contact with the eGene (TLR5 and ABHD2, respectively), chromatin accessibility (highlighted in green in ATAC-seq track) and eGene expression. ATAC-signal is shown as −log10(p value) pileups determined by Genrich140. Boxplots show the genetic effects of the variant on each modality (boxes show 25th, 50th and 75th percentiles, with upper and lower whiskers to the largest or smallest value no further than 1.5 x the interquartile range from the hinge). The red lines represent the regression lines based on the posterior mean of the regression coefficients of the GUESS model, and the blue lines represent the Maximum Likelihood Estimation (MLE) with a 95% confidence interval. Panels (D) and (E) were plotted using the Plotgardener R package125. Source data for C–E are available on OSF168.
