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BACKGROUND Single-nucleotide polymorphisms (SNPs) are important indicators of susceptibility to breast cancer. OBJECTIVE To assess the association between SNPs in the FAM13A, PHLDB1, and CYP24A1 and breast cancer risk in the Chinese Han population. METHODS A case-control study including 379 female breast cancer patients and 407 female healthy controls was performed. SNPs were genotyped using Agena MassARRAY platform. The χ2 test was used to compare allele, genotype and haplotype frequencies between case and control groups. Genetic models and haplotype analyses to assess the association between SNPs and breast cancer risk by computing odds ratios (ORs) and 95% confidence intervals (CIs) using logistic regression. RegulomeDB and HaploReg databases were used to calculate possible functional effects of polymorphisms. RESULTS Overall analysis results showed that rs4809957 was associated with an increased risk of breast cancer (allele A: OR= 1.27, 95% CI: 1.03-1.55, p = 0.024; AA vs. GG: OR = 1.80, 95% CI: 1.15-2.82, p = 0.010; recessive model: OR = 1.70, 95% CI: 1.12-2.58, p = 0.012); and rs1059122 was associated with a reduced breast cancer risk in the recessive model (OR = 0.71, 95% CI: 0.51-0.98, p = 0.039). Stratification analysis found significant associations between the three SNPs (rs1059122, rs17748, and rs4809957) and breast cancer risk. CONCLUSION Our results suggest that rs1059122 (FAM13A), rs17748 (PHLDB1), and rs4809957 (CYP24A1) may play an important role in the development of breast cancer in the Chinese Han population. Future studies will identify both population replication and functional validation to confirm our findings.