The DNA sequence, which is more common among people with Indian Asian than European ancestry, is found in around half of the population and sits close to the MC4R gene, which regulates the body's energy levels by influencing the intake of food and the expenditure of energy.
The new genetic variants were identified during a study involving 90,000 people and individuals with two copies appear to be around 1.5kg heavier.
The effects of the new gene add to those of the FTO gene, which was recently reported to influence weight.
According to experts, people who carry both the FTO variant and the new variants tend to be around 3.8kg heavier than average.
Senior author Dr Ines Barroso, a researcher at the Wellcome Trust Sanger Institute, commented: "The precise role in obesity of genetic variants in FTO and near MC4R remains to be discovered, but we can now begin to understand the biological consequences of these variants. This is where this research will make a difference."