Professor David Reich of Harvard Medical School, the lead author of the study, said: 'Now that we can estimate the probability that a particular genetic variant arose from Neanderthals, we can begin to understand how that inherited DNA affects us'.
The researchers compared the genomes of 1,004 people of European and Asian descent with Neanderthal DNA from a 50,000-year-old toe bone found in a Siberian cave. These genomes were also compared to those of 176 West Africans. Ancestors of people from that part of the world are thought never to have interbred with Neanderthals.
In contrast, between two percent and four percent of the modern non-African genome is considered to be a result of ancient Homo sapiens interbreeding with Neanderthals.
The researchers in this study found that Neanderthal DNA is not evenly distributed throughout the genome - some areas are particularly rich, whereas in other areas it is almost entirely absent. Neanderthal DNA was found in very low quantities in regions of the X chromosome and in testes-specific genes, for example.
However a number of genetic variants inherited from Neanderthals were linked to diseases, especially autoimmune disorders such as lupus, biliary cirrhosis (an autoimmune disease of the liver), Crohn's disease and type 2 diabetes.
One question the scientists are considering is whether our ancient relatives also had these diseases or whether the variants only impact health in a modern genetic setting. Currently, says Dr Sriram Sankararaman, one of the study's scientists, 'we don't have the fine knowledge of the genetics of Neanderthals to answer this'.
The answer might come with further research. In a statement, the scientists say they are now searching for Neanderthal mutations in a 'biobank containing genetic data from half a million Britons', presumably UK Biobank.