Fig. 4
Immune response modifies genetic associations to disease. a Manhattan plots of eQTL (top panels) and disease (middle panels) p-values in colocalized loci. The bottom panels show the dynamics of corresponding eQTL effect sizes in different conditions. b Two additional GWAS loci colocalize when the mean of gene expression across all seven conditions is used to map eQTLs (see Methods section). c Overlap of GWAS SNPs that are in high LD (r 2 > 0.8) with reQTLs in monocytes with disease phenotypes connected to reQTL genes and corresponding immune stimulations. Supplementary Data 4 for trait abbreviations. d Genome-wide enrichment of reQTL and ceQTL associations in autoimmune GWAS with 95% confidence intervals (left panel), and Quantile–quantile (Q–Q) plots for SLE (middle panel) and Celiac disease (right panel). Supplementary Fig. 10b for additional Q–Q plots, and Supplementary Fig. 11 and Supplementary Fig. 12 for results of non-autoimmune traits
