Coding-synonymous SNPs (neutral SNPs) have a low frequency of base-transversion alleles. Risk SNPs exhibit a low GC-content background and are associated with a low DNA methylation level, while neutral SNPs associate with high GC-content and high DNA methylation. A: Average nucleosome occupancy against GC-content around SNPs sites; B: Observed allele frequencies of SNPs in humans. Neutral SNPs refer to coding-synonymous SNPs. The different significant P-values are indicated. Base transition refers to A/G and C/T substitution; base transversion refers to G/T, A/C, C/G and A/T. The Base transition is three-fold higher than that of base transversion in SNPs; C: GC-content profile around neutral SNPs and risk SNPs sites; D: DNA methylation levels around neutral SNPs and risk SNPs sites.