Fig. 6

hQTLs alter eQTL gene expression within chromatin networks. Quadrant plots for statistically significant interactions with genes within the HLA region (a) and outside the HLA region (b). Each statistically significant (FDR < 0.05%) distal interaction is represented by a point oriented by the value of coefficients in the generalized linear model for the eQTL main effect (x-axis) and the interaction effect (y-axis). The sign and magnitude of the coefficients determine the directionality and strength of the two effects on the eQTL target gene’s expression. The total number of interactions within each quadrant are labeled. c Example of ICOSLG triplet interaction with eQTL rs56124762 and hQTL rs8134436. d Example of BLK triplet interaction with eQTL rs10098664 and hQTLs rs13256690. For both c and d, 3D topology map with H3K27ac looping data is represented by red loops. H3K27ac ChIP peaks are in blue and anchored to looping data. hQTLs (black dots), eQTLs (orange dots), and gene locations are presented. Scatterplots of the eQTL genotypes alone (left panel) and stratified by the hQTL genotypes (right panel) are given