A genome-wide association study in Chinese twins was performed to explore associations between genes and pulse pressure (PP) in 2012, and detected a suggestive association in the phosphatase and actin regulator 1 (PHACTR1) gene on chromosome 6p24.1 (rs1223397, P = 1.04e-07). The purpose of this study was to investigate associations of PHACTR1 gene polymorphisms with PP in a Chinese population. We recruited 347 subjects with PP ≥ 65 mmHg as cases and 359 subjects with 30 ≤ PP ≤ 45 mmHg as controls. Seven SNPs in the PHACTR1 gene were genotyped. Logistic regression was performed to explore associations between SNPs and PP in codominant, additive, dominant, recessive and overdominant models. The Pearson's χ2 test was applied to assess the relationships of haplotypes and PP. The A allele of rs9349379 had a positive effect on high PP. Multivariate logistic regression analysis showed that rs9349379 was significantly related to high PP in codominant [AA vs GG, 2.255 (1.132-4.492)], additive [GG vs GA vs AA, 1.368 (1.049-1.783)] and recessive [AA vs GA + GG, 2.062 (1.051-4.045)] models. The positive association between rs499818 and high PP was significant in codominant [AA vs GG, 3.483 (1.044-11.613)] and recessive [AA vs GG + GA, 3.716 (1.119-12.339)] models. No significant association of haplotypes with PP was detected. There was no significant interaction between six SNPs without strong linkage. In conclusion, this study presents that rs9349379 and rs499818 in the PHACTR1 gene were significantly associated with PP in Chinese population. Future research should be conducted to confirm them.

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