Fig. 6. Examples of context-specific eQTL informative for disease risk.

(A) Local association plot showing evidence of cis-eQTL for CARD9 in naïve cells. After conditioning for rs4078099, no evidence of association is seen. (B) After induction with IFNγ, in addition to the eQTL tagged by rs4078099, a second stimulus-specific independent peak of association is tagged by rs36119806. (C) Local association plots for CD with SNPs colored as per (A) and (B). The lead SNP rs40771515 is in high LD with rs4078099 (r² = 0.93); after conditioning, a second independent GWAS peak is seen (lead SNP rs11145766, r² = 0.84 with rs136119806). (D) Box plots showing expression of CARD9 by allele in naïve cells, and after IFNγ stimulation, showing allelic association by SNP corrected for the effect of the other eQTL or by combination of inherited alleles for rs4078099 and rs36119806. (E) rs3859192 is the peak eQTL for expression of GSDMA, a transforming growth factor–β–regulated proapoptotic gene. (F) Local association plot for GSDMA expression after 2-hour LPS using imputed genotyping. (G) Allele-specific correlation for expression values per genotype demonstrates significant regulation of GSDMA expression in homozygous carriers of the C allele by the solute transporter SLCO2B1 after 2-hour LPS with no association being present in homozygous carriers of the T allele. Similar results were obtained analyzing monocytes after 24-hour LPS, and with both probes to SLCO2B1, with no association observed in the naïve state.