Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation
Fig 4
An example of a gene harboring four independent cis-eQTL signals.
The top left panel plots the cis-SNPs with PIP ≥ 0.02. The locations of the SNPs are labeled with respect to the TSS of gene LHPP. The ticks on the x-axis indicate all interrogated cis-SNPs in the region. The SNPs with the same color are in high LD and represent the same eQTL signal. In the plot, the sums of the PIPs from the SNPs in the same colors are all ∼ 1, indicating that we are confident of the existence of each signal. The heatmaps show the LD patterns in each of the population group. They are qualitatively similar, except that the SNPs representing the first signals are monomorphic in GBR. In the bottom panel, we plot the effect sizes of eQTLs jointly estimated from one of the high posterior probability models. Each of the SNP plotted belongs to a different colored cluster in the PIP plot (as indicated by the color coding of the error bars). The effect sizes and standard errors are estimated from the multiple linear regression models (containing all four SNPs) separately fitted in each population group. All the signals show strong effect size consistency across populations.