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Background  The  FTO  gene has recently become one of the most extensively investigated genes associated with body mass and has been shown to play a role in cardiovascular diseases as well. The aim of the current study was to investigate the effect of a common variant of  FTO  gene, rs9939609 in obese and coronary heart disease (CHD) patients of Pakistan and investigate whether it has any influence on the serum biochemical parameters.    Methods  A total of 970 samples (295 obese, 425 CHD and 250 controls) were genotyped using TaqMan allelic discrimination assay. Serum total cholesterol, HDL-C and triglycerides were measured using spectrophotometric methods. LDL-C was calculated by Friedwalds equation. Statistical analysis was done by SPSS version 22.    Results  Results showed moderately high minor allele frequency (MAF) in obese and CHD cases as compared to controls (obese = 0.381 CAD = 0.361 and controls = 0.286). The variant was significantly associated with obesity and CAD (obesity odds ratio (OR) = 1.54, confidence interval (CI) = 1.07–2.21,  p  = 0.0009; CHD OR = 1.43, CI = 1.02–2.01,  p  = 0.004) in Pakistan. The risk allele did not show a significant association with any of the lipid trait tested ( p  > 0.05) but a strong association was observed with plasma glucose levels (obese  p  = 0.001, CAD  p  = 0.014, controls  p  = 0.019).    Conclusion  In conclusion, the variant was associated with obesity and CAD in the studied subjects and its possible effect may involve the blood sugar metabolism but not serum lipid chemistry.    Electronic supplementary material  The online version of this article (doi:10.1186/s12944-016-0200-0) contains supplementary material, which is available to authorized users.

lipids in health and disease

Role of a common variant of Fat Mass and Obesity associated (FTO) gene in obesity and coronary artery disease in subjects from Punjab, Pakistan: a case control study