In CRY1 CpG2 and CpG5 and in CLOCK CpG1, increasing levels of methylation tended to be associated with lower odds of breast cancer, with odds ratios (OR) of 0.88 (95% confidence interval (CI) 0.76–1.02), 0.84 (95% CI 0.74–0.96), and 0.80 (95% CI 0.68–0.94), respectively. This evidence concerns the gene CLOCK and breast cancer.