Probe-level differences between CD4⁺ and CD8⁺ T cells in the CTLA4 gene.

(A) Overview of the CTLA4 gene locus. On the top panel the SNPs associating with different isoform levels between the two cell types in the CTLA4 gene are depicted as grey bars, the gene transcripts are drawn, and the positions of the three gene expression probes and four CpG sites in the region are shown at the bottom. (B) The expression levels (y-axis, quantile normalized and log₂ transformed) for each of the probes are shown by boxplots for CD4⁺ and CD8⁺ T cells. The mean of the differences in expression levels between CD4⁺ and CD8⁺ T cells are estimated by linear mixed models. (C) Methylation levels (y-axis) for each of the CpG sites along the genomic position (x-axis) are shown by boxplots for CD4⁺ and CD8⁺ T cells. Medians of the methylation values per CpG sites are connected by a line in both cell types. The mean of the differences in methylation levels between CD4⁺ and CD8⁺ T cells are estimated by linear mixed models. Only estimates with P-value < 0.05 are marked on the figure. (D) Correlation between methylation and gene expression levels are shown on the scatter plot between the differentially methylated CpG site cg26091609 for CD4⁺ and CD8⁺ T cells (y-axis) and three expression probes (x-axis). (E) The effect of rs3087243 on the expression levels (y-axis, residual gene expression levels) of different probes in the CTLA4 gene are shown by boxplots within violin plots depicted as in Fig 1. Effect sizes and corresponding P-values are reported for the multi-tissue and tissue-by-tissue analysis above and below of the violin plots, respectively. Significant eQTLs in the tissue-by-tissue analysis are indicated with a star (*).