Researchers looked at whole genome sequences from 4,000 people in UK and compared this with data about their lipid levels.
They spotted an association between levels of lipids called triglycerides and the presence of the APOC3 gene variant.
The research suggests that people with the rare change (approximately 0.2 per cent of the population carry this) typically have lower levels of triglycerides.
Previous research has shown that lower levels of triglycerides are associated with reduced risk of cardiovascular disease.
"Once we can understand the mechanism of the protective function of this variant, we can try to use this information to develop novel therapies to help those at risk of cardiovascular disease," said Professor Steve Humphries, senior author from University College London.

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