We found strong evidence of positive association of FDPS expression level with breast cancer risk (OR per SD, 0.66; 95% CI, 0.49–0.83; P = 9.77 × 10−7), NSUN4 expression level with both breast cancer risk (OR per SD, 1.05; 95% CI, 1.03–1.07; P = 5.24 × 10−6) and prostate cancer risk (OR per SD, 1.06; 95% CI, 1.03–1.09; P = 1.01 × 10−5), NSUN4 methylation level with both breast and prostate cancer risk, and VARS2 methylation level with lung cancer risk. Here, NSUN4 is linked to breast cancer.