In this study we genotyped three Asian ethnic populations in Singapore for two polymorphisms of the CETP gene to determine their allele frequencies and association with CAD and plasma lipid levels. The allele frequencies of the Taq1B polymorphism showed marked ethnic differences. The B1 allele is most common in the Malays but is the minor allele in the Indians. The minor B2 allele in the Chinese and Malays are close to most Caucasian frequencies reported . The allele frequencies of Taq1B polymorphism in Indians, Malays and Chinese are consistent with the respective studies conducted previously in Sri Lankans , Taiwanese  and Singaporeans . Similar to B1, the -629C allele is also the most common in the Malays (0.60) but is the minor allele in the Indians (0.30).
Among the three major ethnic groups in Singapore, the Chinese is the only group that shows a significantly lower frequency of the B2 allele in CAD + cases compared to the controls. This finding is consistent with observation in the Caucasians  and suggests the association of the B2 with some protective factors of CAD in Chinese population. Chinese subjects without the B2 allele have 2.0 times higher risk of CAD relative to those who have at least one copy of the B2 allele. This is independent of the effects of age, smoking, BMI, gender, hypertension, dyslipidemia and diabetes mellitus. However, this effect is not observed in the Malays and Indians. In the Taiwanese, the odds ratio for CAD was slightly higher for the B1B1 than B2B2 group, but no significant difference in Taq1B allele distribution was observed between the control and CAD groups . Padmaja et al.  demonstrated that CETP B1B1 of Taq1B was significantly associated with increased risk for CAD (OR 2.7; 95% CI 1.5-3.3) in the Indian population. The B2 allele is unlikely to be a functional mutation as its position in the intron is not known to affect RNA splicing or serves any other regulatory purposes. As such, any phenotype that it is associated has to be due to its LD with another functional site that is either within the CETP gene or its functionally related genes nearby, such as the lecithin-cholesterol acetyl transferase gene. Dachet et al.  first reported the strong LD between -629C > A and Taq1B polymorphisms. Later many more alleles in the CETP gene [39–41] were also reported to be in LD with the Taq1B site. In the Singaporean population, weak LD between Taq1B and -629C > A was consistently observed in all three ethnic groups, although to varying extent. It is highest in the Malays, followed by Chinese and Indians. Wu et al.  observed a LD between Taq1B and -629C > A polymorphic sites in the Chinese population from China.
The effect of the Taq1B intronic polymorphism in this study could not be generalized across ethnic groups and genders. This is expected since the magnitude of its effects is dependent upon the strength of its LD with a functional site. Among the lipid traits that we have studied, the B2 allele is most evidently associated with raised levels of protective factors such as HDL-C and its associated apoA1. This trend of association was consistent in all ethnic groups and genders although statistical significance was attained only in the Chinese men. Significant association of the B2 allele with elevated HDL-C was also reported for the Framingham population , Chinese population , Iranian population [19, 20] and Tunisian population . In their studies, the protective effects of the B2 allele on the development of CAD were observed in association with increased HDL-C and decreased CETP activity. The association of the B2 allele with higher plasma HDL-C and / or apoA1 has been consistently observed in many other studies [15, 24, 27, 28, 33, 42] as well. However, Rahimi et al.  indicated that the CETPB1 allele is associated with increased risk of CAD and type 2 diabetes mellitus independent of plasma HDL-C level in the Iranian population.
In this study, we have shown that the association of the Taq1B site with HDL-C and apoA1 levels remains independent of the effects of the promoter -629C > A. Both sites have similar effects on apoA1. We asked the question of whether the -629C > A site is the functional mutation while Taq1B was merely showing significant association with plasma lipid levels as a result of LD. We concluded that this may not be the case. Firstly, a functional mutation is likely to have its effect observed across all ethnic groups and genders. However, we observed effects of the promoter polymorphism only in Chinese men. Although we cannot be conclusive that the -629C > A polymorphism is not a functional mutation since other genes and environmental factors could have masked its moderate effect, its ethnic-and gender-specific effects nevertheless suggests the unlikelihood of this being so. Secondly, the strength of association with HDL-C and apoA1 levels was consistently higher for the Taq1B site than the promoter site. This should not be the case if the -629C > A site is functional and Taq1B site its marker. Moreover, in the two-way ANCOVA, there was no effect of the promoter polymorphism when the Taq1B site was included in the model. We postulated that there could be other functional sites within or near the CETP gene that the Taq1B site is in stronger LD with than the promoter site. Both Taq1B and -629C > A polymorphisms could possibly have independent effects on HDL-C and apoA1 levels and hence they do not show significant effects individually when they are included in the same 2-way ANCOVA model. In the Turkish population, it was found that CETP -629C > A polymorphism was not associated with CAD . As with any complex traits, the genotypic effect is usually confounded by environmental factors. In this study, we found significant gene-environmental interaction of the Taq1B polymorphism with BMI and smoking. The protective effect of the B2 allele was only observed in subjects having BMI <23 and in non-smokers. This is consistent with other studies that examined the confounding effects of BMI [21, 28, 38] and smoking [15, 25, 38, 44].
We concluded that, i) the absence of the B2 allele was associated with CAD in the Chinese, ii) the minor alleles of the two polymorphisms were significantly associated with higher plasma HDL-C levels in the Chinese men (B2), iii) the effects of the polymorphisms were significant only in non-smoking subjects with BMI up to the 50th percentile, iv) The effect of the Taq1B polymorphism is not entirely dependent on the -629 C/A site but that it could be in LD with some other functional sites.