The mutation of the DNA sequence would alert the level and pattern of gene expressions, and even had risk of complex disease. With the development of next-generation sequencing technology, the association between genetic variation and epigenetic modification, such as DNA methylation has been widely concerned. Integration analysis of genetic variation and DNA methylation plays an important role in understanding the regulation mechanisms of epigenetics and the pathogenesis disease. We discussed

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... e progress about genetic variants associated with DNA methylation, including the relationship between genetic variation, DNA methylation and complex disease, the association study of DNA methylation quantitative trait loci (meQTLs) and the expression quantitative trait loci (eQTLs), as well as identification of allele specific methylation, that will be help for understanding the regulatory mechanisms of genetic variation and epigenetic modification.