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Table 2 Predicted impact of SNPs in CpG on methylation readout using Infinium II probes

From: Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies

  1. BCD - bisulfite converted DNA; NR – not relevant (no CpG in the genomic sequence); strikethrough – mismatch between the probe and the interrogated locus; italics – incorporated fluorescently labeled ddNTPs (C, G – green = methylation signal; A, T – red = unmethylation signal); dots adjacent to the 3′-most position of the probe indicate no probe extension; “RC” in the probe sequence represents degenerated sites complementary to under-a-probe CpGs (“YG” in the BCD sequence indicates no assumption of the concordant methylation with the interrogated dinucleotide)
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