Genetic variation in the PEAR1 locus is linked to platelet reactivity and cardiovascular disease. The major G-allele of rs12041331, an intronic CpG-SNP, is associated with higher PEAR1 expression in platelets and endothelial cells than the minor A-allele. The molecular mechanism underlying this difference remains elusive. We have characterized the histone modification profiles of the intronic region surrounding rs12041331 and identified H3K4Me1 enhancer-specific enrichment for the region that covers the CpG-SNP. Interestingly, methylation studies revealed that the CpG site is fully methylated in leukocytes of GG carriers. Nuclear protein extracts from megakaryocytes, endothelial cells vs. control HEK-293 cells show a 3-fold higher affinity for the methylated G-allele, compared to non-methylated G or A alleles in a gel EMSA. To understand the positive relationship between methylation and gene expression, we studied DNA methylation at 4 different loci of PEAR1 during in vitro megakaryopoiesis. During differentiation the CpG-SNP remained fully methylated, while we observed rapid methylation increases at the CpG-island overlapping the first UTR exon, paralleling the increased PEAR1 expression. In the same region, A-allele carriers of rs12041331 showed significantly lower DNA methylation at CGI1 compared to GG homozygote. This CpG-island contains binding sites for the methylation-sensitive transcription factor CTCF, whose binding is known to play a role in enhancer activation and/or repression. In conclusion, we report the molecular characterization of the first platelet function-related CpG-SNP, a genetic predisposition that capacitates PEAR1 enhancer activity through allele-specific DNA methylation.