Figure 5.
Population-Specific eQTLs May Underlie ieQTL Regulating C12orf54
The interaction between rs2731091 and rs4760707 regulating C12orf54 replicated but was not nominally significant (p < 0.05) in any population in the stratified analysis.
(A) Due to the population normalization procedure, there are not systematic differences in the expression of C12orf54 between populations; however, we found that each variant was a population-specific cis-eQTL.
(B) rs4760707 was a cis-eQTL in CHB+JPT (p = 7.25 × 10−6) but not in YRI (p = 0.17) or CEU (p = 0.96).
(C) rs2731091 significantly regulated gene expression as a cis-eQTL in YRI (p = 7.28 × 10−6) but not CEU (p = 0.14) or CHB+JPT (p = 0.84).
(D) There were clear population differences in the frequency of two-locus genotypes between populations; in combination, it appears the population differences in two-locus genotypes and population-specific cis-eQTL produced a nuanced form of population stratification.