one of the best studied read outs of epigenetic change is the differential expression of imprinted genes controlled by differential methylation of imprinted control regions icrs to address the impact of genotype on the epigenome we performed a detailed study in 128 pairs of monozygotic mz and 128 pairs of dizygotic dz twins interrogating the dna methylation status of the icrs of igf2 h19 kcnq1 gnas and the non imprinted gene runx1 while we found a similar overall pattern of methylation between mz and dz twins we also observed a high degree of variability in individual cpg methylation levels notably at the h19 igf2 loci a degree of methylation plasticity independent of the genome sequence was observed with both local and regional cpg methylation changes discordant between mz and dz individual pairs however concordant gains or losses of methylation within individual twin pairs were more common in mz than dz twin pairs indicating that de novo and or maintenance methylation is influenced by the underlying dna sequence specifically for the first time we showed that the rs10732516 a polymorphism located in a critical ctcf binding site in the h19 icr locus is strongly associated with increased hypermethylation of specific cpg sites in the maternal h19 allele together our results highlight the impact of the genome on the epigenome and demonstrate that while dna methylation states are tightly maintained between genetically identical and related individuals there remains considerable epigenetic variation that may contribute to disease susceptibility.