Fig. 5: Evidence for causal relationships at trimodal QTLs.

A The causal mediation strategy. B–D Overview of the three types of models considered. E, F Example of Model I with full mediation. Plot E summarises the Average Causal Mediation Effect (ACME), Average Direct Effect (ADE) and Total Effect (TE) (dot—mean effect, lines—95% bootstrap confidence intervals; non-significant if spanning 0; two-sided p values were computed using the non-parametric bootstrap procedure in the R package mediation¹⁵⁸). The ADE confidence interval spans zero, indicating full mediation. Plot (F) shows the three modalities in the mediation model: SNPs/haplotype, i.e. the genetic variants in the GUESS set X, the ATAC-seq signal as a mediator M and chromatin contact with the eGene promoter as the outcome Y. G CRISPRi at the cQTLs in the THBS1 locus. Top left: Change in ATAC-seq signal at the ___location of CRISPRi perturbation (grey lines show dCas9-KRAB target regions). The black line shows the change in ATAC-seq in CRISPRi U-937 cells with locus-targeting versus non-targeting gRNAs (rlog reads, mean of three biological replicates), grey ribbon represents standard deviation and red line shows top 5% change across a 2 Mb window. Top right: CRISPRi-induced change in ATAC-seq at the canonical THBS1 promoter. Bottom: CRISPRi-induced change in mean 4C-seq signal (N = 3 per condition). Vertical grey bars show the viewpoints at the cQTLs and THBS1; the black arrow highlights 4C-seq signal at THBS1 promoter (difference not statistically significant, FDR-adjusted p value = 0.66). H Left plot: a global shift in contact directionality from the cQTL region within a 2 Mb window. Right plot: the shift observed in allele-specific 4C seq in primary monocytes (three heterozygotes for cQTL rs2033937). I qPCR-detected fold change in THBS1 expression in CRISPRi cells versus control cells (N = 3). The p value is from a two-sided, paired T-test on ΔCt values (Supplementary Fig. 6C). J–M Examples of full mediation in Models II and III, respectively, similar to (E, F). F, G, K, M used the Plotgardener R package¹²⁵. Source data for E, G–J, L are available on OSF¹⁶⁸.