Fig. 5

Examples of an ambiguous impact of SNP on the distribution of β values. Upper panel: Individual β values for 36 cell lines examined using the type II probe (cg14175932) interrogating CpG site with a SNP(C>T) at the first position. Low β values observed in most of the East Asian cell lines are concordant with the predominant presence of TpG alleles (yellow) in this population. The dispersed, intermediate β values observed in European population correspond to cell lines with CpG (blue) and CpG/TpG (red) genotypes; grey tags denote genotypes not confirmed experimentally. The varying β values for heterozygotes and CpG homozygotes indicate partial methylation status of the CpG alleles. Lower panel: Fluorescence readouts for the probe cg14175932 (Infinium II). Cell lines with homozygous TpG genotypes display strong red and no green signal, mimicking unmethylated status; heterozygotes have nearly-equal, medium-range intensity of both red and green fluorescence signals; all lines with homozygous CpG genotypes display similar green and red signal, indicating non-uniform methylation status