Fig. 6
From: “Gap hunting” to characterize clustered probe signals in Illumina methylation array data
Effect of probe SNPs on methylated signal and unmethylated signal in Type II probes. We isolated specific probes that met the following conditions: it contained a measured SNP in the 50 bp probe length outside of the C, G and/or SBE sites, and it contained only a single SNP in the probe length. The probes that met our criteria varied in distance from 1 to 50 base pairs from the interrogated CpG site. At each distance value, we plotted the mean (shown by dotted lines) and inter-quartile range (grayed area) of the people who were homozygous for the reference allele (shown in red), heterozygous (shown in green) or homozygous for the minor allele (shown in blue). Lack of signal concordance across these 3 groups indicates stronger SNP influences on signal. For both methylated (a) and unmethylated signals (b), polymorphisms closer to the C site show stronger influences on signal. The influence is strongest up to approximately 10 bp but is observed up to roughly 20 bp from the measured C site