The study of 5000 children, led by University of Auckland researchers, found those with the gene variant, particularly boys, were more likely to be heavier and taller than others at age 4.
Those children were about 400g heavier than the other children, almost 1cm taller and had a waist circumference almost 1cm larger.
Berry said the increase in weight was significant given the average weight of a 4-year-old was 19-20kg.
She said the findings also suggested that, while genetics played a part, a child's environment could change the effect of the gene variant.
There was no difference in size among children with the CREBRF variant when they were born or when they were 2 which suggested diet and activity levels could play a part - although more research was needed to prove that, she said.
"What we are seeing is the effect of the gene becoming more apparent as time goes on. We could hypothesise that that's because of changes in the environment," Berry said.
She said the research was important for the country because it could help shape the focus of policies on factors that would make the most difference.
"Our research represents an important step toward understanding the interactions between our diet, lifestyle, and genetic make-up," Berry said.
"Being able to look at anonymous, population-level data from Growing Up in New Zealand provides us with the unique opportunity to figure out why people are the way they are, and to create new opportunities for improving health outcomes."
She said the new knowledge offered the chance to implement evidence-based interventions aimed at establishing healthy growth from the earliest possible age.
Healthy habits
Family rules and routines about food and screen time could help fight the wave of obesity, a University of Otago study has found.
Lead researcher Dr Tasileta Teevale said the team talked to 68 parents from 30 Pacific Island families in a low socio-economic neighbourhood to find out what they were doing to keep themselves healthy.
There were three differences between families with an obese adolescent and a healthy-weight child.
• Parents with healthy-weight children regularly ate breakfast and lunch while parents of obese children often skipped these meals due to time constraints and work commitments and children matched their parents' eating habits. Obese children often substituted breakfast at home with high-energy store-bought food, such as fizzy drink and a pie, as breakfast on-the-run.
• Parents with healthy-weight children had specific, strict, household food rules, such as banning fizzy drinks, cooking homemade meals, and not buying junk food.
• Households with healthy-weight children had rules limiting screen time.
Teevale said the research, funded by the Health Research Council, showed the solution lay with the community and that individual families could make a difference.
The factors highlighted by the study could also be applied to obesity prevention and treatment programmes, he said.