The most discriminative CpGs in the plasma cohort were CpG1/2/4/9/10 for SPAG6, CpG1/2 for PER1 and CpG1/4 for NKX2-6 and ITIH5. SPAG6 showed a significantly increased methylation frequency in breast cancer patients (4.4% versus 7.8%, p = 0.0059) whereas PER1 (2.6% versus 4.8%, p = 0.5792), NKX2-6 (4.6% versus 6.5%, p = 0.0570) and ITIH5 (7.6% versus 6.1%, p = 0.1063) showed a non-significant increase. Here, SPAG6 is linked to breast cancer.