It was noted as far back as 1700 that 'Chairworkers' seemed tp have an increased risk for several diseases.
Since then, prolonged sitting (as a habit or for work purposes) has been found to increase the risks of developing heart disease, obesity, type 2 diabetes and various cancers.
It's currently not known why long periods of sitting seems to increase the chances of developing these diseases.
A 2010 review study found that although there are some well established links between sedentary behaviour and disease, they are probably weaker than was prevously thought.
See : Occupational Sitting and Health Risks, A Systematic Review American Journal of Preventive Medicine, Vol. 20, Issue 4.
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