Fig. 5: Interaction between DNA methylation and expression.

a Circos plot of LPS-specific g/tQTL-mQTL pairs that share one causal variant affecting both gene/transcript expression and methylation level. Gene/transcript and methylation sites are present on each track in g/tQTL-mQTL pairs of monocytes that are stimulated by LPS. Different colours are utilised to enhance readability. Ribbons link genes, transcripts, and methylation sites that have a causal variant together. The chromosome and genomic coordinates should be indicated on the outer track. b rs2914937 influences the methylation level (mQTL) and gene expression (gQTL) in LPS-stimulated monocytes. c Read coverage plot for CD55 gQTL in LPS-stimulated monocytes. The lead SNP (rs891378) is in LD with rs2914937 (R² 0.99). d Expression of CD55 correlates with the cg22687766 methylation site. The CD55 expression and cg22687766 methylation, coloured by SNP rs2914937 genotype. Each data point on the horizontal and vertical axis indicates values for a single sample. Regression lines are shown for categories of genotypes. The adjusted p-value for the beta coefficient correlation between methylation and expression independent of the genotype is 4.56 × 1⁻⁶. e Highlighted isoforms of CD55, including ENST00000367063 and ENST00000314754, show a significant switch in isoform usage across the LPS-stimulated condition. The display of splice junctions is limited to those that are not present in all transcripts. f rs2914937 influences CD55 transcripts ENST00000367063 and ENST00000314754 most significantly post LPS. g Expression of CD55 transcripts (ENST00000367063 and ENST00000314754) correlates with the cg22687766 methylation site. The transcript expression and cg22687766 methylation level are coloured by the genotype SNP rs2914937. Abbreviations: “N” represents and lists the specific number of donors. The x-axis of the boxplot represents the different alleles of the SNP that are related to the expression. Each box indicates a particular SNP allele, and the y-axis displays the expression levels of individuals with that allele. The normalised read count and Fragments Per Kilobase Million (FPKM) metrics display the expression levels of genes and transcripts, respectively.