Probes targeting polymorphic CpGs may affect the assessment of DNAm. (A) A documented SNP was identified at the target C or G position of 4.3% of 450 k probes (target CpG SNP). Of these SNPs, 43.2% had a heterozygosity of >0.1 and due to their frequency in the population are more likely to affect measurement of DNAm. (B) Using blood samples (n = 4) as example, the SD in ß value between individuals was calculated for all probes. Probes with small SD in ß (<0.10) were removed from the analysis. The distribution of SD in ß value was plotted for all probes, and for the subsets of probes annotated with a target CpG SNP, a SNP within 10 bps of the target but without a target CpG SNP (SNP <10 bp) and a SNP within the remainder of the probe (SNP >10 bp). Numbers in brackets indicate Kolmogorov-Smirnov (KS) statistics in comparison to the distribution of all probes. (C) Using a selection of 261 adult blood samples extracted from the aging dataset [GSE:40279], the distribution of SD in ß value was plotted for the subsets of probes as described in (B). Numbers in brackets indicate KS statistics in comparison to the distribution of all probes. (D) DNAm at probe cg06961873 across 12 individuals exemplified the trichotomous pattern of DNAm hypothesized at a target CpG SNP. The three distinct levels of DNAm corresponded to sample genotype at SNP rs61775206, located at the target CpG: TT genotypes were assessed as hypomethylated, TC genotypes as approximately 50% methylated and CC genotypes as close to fully methylated. 450 k, Infinium HumanMethylation450 BeadChip; DNAm, DNA methylation.