I wish this link is useful 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906547/

Researches have shown that regular aerobic exercises can lead to changes in DNA methylation in 18 genes associated with obesity and in 21 genes associated with type 2 diabetes. A handful of those genes also had changes in mRNA expression, potentially suggesting that exercise could impact adipocyte metabolism.

Metabolic disorders are influenced by genetic and environmental factors, and epigenetic factors such as DNA methylation could help explain how the environment influences the genome, ultimately impacting metabolism.

No doubt that the effects of smoking in some mechanisms regulating HDL-Cholesterol primarly reverse Cholesterol transport  play a strong role. HDL-Cholesterol contributes to remove cholesterol excess from blood vessels , moving it into the liver, where cholesterol is excreted by bile. So doing, HDL-Cholesterol impedes LDL-Cholesterol oxidation and oxidized LDL-Cholesterol is the major precursor of atherogenesis. It is Worth noting that aerobic exercise,, regularly performed, increases HDL-Cholesterol levels.

This question is very interesting as it reflect the duality of smoking and aerobic exercice in cardiovascular system. It's well known that current smokers have low HDL-C ( a cardiovascular protector) and that aerobic exercice reduce Ldl-C. Smokers who perform regular aerobic exercice have also reducing of total level cholesterol.

This reference may help you: "The Effects of 8-Weeks Aerobic Exercise Program on Blood Lipids and Cholesterol Profile of Smokers vs. Non Smokers

By Taifour, Akef; Al-Shishani, Ahmad; Khasawneh, Aman; Al-Nawaiseh, Ali; Bakeer, Mohammed"

I am of the same view as Dr. Aurelio Leone and endorse his comments.

I am of the same view as Dr. Aurelio Leone and endorse his comments.