DNA methylation and its consequences. (A) DNA methylation and TET mediated DNA demethylation. Cytosine (C) is methylated at 5th carbon of the pyrimidine ring by DNA methyltransferases (DNMT) to form 5-methylcytosine (5-mC). Ten-Eleven Translocation (TET1-3) enzymes sequentially act on 5mC to generate 5 hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), and finally 5-carboxylcytosine (5-caC). The 5fC and 5caC are excised directly by thymine DNA glycosylase (TDG). The resulting abasic sites, which are generated by TDG since it has the ability to catalyze the glycosidic bond between the base and deoxyribose sugar of DNA, are eventually replaced with unmethylated cytosines by base excision repair (BER). (B) Relationship between SNP, CpG site, eQTLs, mQTLs, and neurodegenerative diseases. Genome-Wide Association Studies (GWAS) have identified several Single-Nucleotide Polymorphisms (SNPs) which indicate differences in the inheritance of diseases. The single base pair changes in the DNA sequence can affect the gene expression levels and referred to as expression quantitative trait loci (eQTLs). Methylation quantitative trait loci (meQTLs) are the individual DNA sequence variation at specific loci that can cause changes in DNA methylation patterns of CpG sites. Significant correlation of methylation mark with gene expression is termed as expression Quantitative Trait Methylations (eQTMs). Recent studies have shown that eQTLs, meQTLs, and eQTMS are linked with neurodegenerative diseases. (C) Differential CpG methylation and its association with neurodegenerative diseases.