Fig. 4

Validation of methQTL at PON1 locus using ultra-deep bisulfite sequencing. A Bisulfite sequencing read pattern maps for three individuals with genotypes homozygous for the reference allele (AA), heterozygous (AG), or homozygous for the alternative allele (GG) for B cells and T cells, respectively. Each line is a sequencing read, where the red color indicates a cytosine, i.e., a methylated cytosine before bisulfite conversion, and blue a thymine, i.e., an unmethylated cytosine before bisulfite conversion. All cytosines within the amplicon are shown in the pattern map and the CpG and CpA dinucleotides are marked. The genotype at rs705379 per sequencing read is indicated on the right. Shown is the common methQTL at the PON1 locus at chr7:94,953,722–94,954,184 (hg19). B Average DNA methylation levels across all samples of the same genotype and standard deviations across the samples. The barplots are shown for all 22 CpGs present in the amplicon. C Average DNA methylation levels across all sequencing reads per sample for the three CpGs that were associated with the SNP genotype in the microarray data analysis for B cells and T cells