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Table 1 Allele-specific methylation of amplicons among individuals and correlation with genotype

From: Non-imprinted allele-specific DNA methylation on human autosomes

  Genes and amplicons
  C21orf81 HSF2BP RIPK4 CBR1
  23_1 23_2 262 232 176_1 176_2
Length (bp) 370 426 400 241 302 476
CpG sites 31 26 42 25 31 44
SNP (strand) dbsnp build 129 A/C (-) rs2297246 A/C (+) rs56270809 A/G (-) rs2838343 A/G (+) rs55860816 del/no del (+) rs41563015 C/G (+) rs25678
Individuals studied 38 19 33 36 21 21
Individuals with SNP 17 8 20 11 1 8
Individuals with SNP and ASM 8 7 19 3 1 1
Coupling of ASM and genotype Always: C hyper- methylated Always: C hyper- methylated 18 cases: G hyper- methylated in right part of amplicon Always: G hyper- methylated Always: del hyper- methylated Always: C hyper- methylated
    1 case: A hyper- methylated in left part of amplicon    
Average allelic methylation difference in ASM cases 53% 60% 54% (G hyper- methylated), 64% (A hyper- methylated) 39% 50% 60%
Individuals with SNP but without ASM 9 1 1 8 0 7
Individuals without SNP 21 11 13 25 20 13
  1. ASM, allele-specific methylation; CpG, cytosine-guanine dinucleotide; SNP, single nucleotide polymorphism.