Background: Hypertension is a medical condition that often occurs parallel to diabetes and obesity. Previously, the role of fat mass and obesity associated (FTO) gene rs9939609 polymorphism (c.46-23525T>A) with obesity has been reported while prevalence and etiological differences exist among different regions and ethnic groups.

Aim: To investigate the association of FTO rs9939609 SNP with hypertension in Pakistani population.

Study design: Cross-sectional study.

Place and duration of study: Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan from 1^st January 2019 to 31^st December 2020.

Methodology: One hundred and ten diagnosed hypertension patients along with 128 healthy volunteers were selected randomly. The single nucleotide polymorphism was analyzed using Amplified Refractory Mutation System-Polymerase Chain Reaction.

Results: In hypertension patients, females were found to be relatively more affected and average blood pressure lies in stage 1. However, we found no significant difference in genotypic frequencies of FTO rs9939609; TT (22.6%), AA (39.6%) and AT (37.8%) and TT (17.18%), AA (39.06%), and AT (43.75%) among HT and controls, respectively. The p and OR values for risk type genotype (AA) are 0.4697 and 0.7700 (95% CI=0.3788-1.565), respectively. Subsequently, the high percentage (60.0 %) of risk genotype (AA) was found in obese-body mass index in hypertension patients.

Conclusion: FTO rs9939609 single nucleotide polymorphism may not be a genetic risk factor associated with onset of hypertension directly and is linked with obesity in Pakistani patients.