You probably use a medium which is a buffer and generally when the ppCO2 varies, the pH vary which modifies the growth of most of the cell lines (especially if your buffer is at base of bicarbonate (HCO3 -)
Almost all CO2 incubators have digitally regulated gas flow inlets. In my opinion you should try to grow the cells in absence of CO2 first (i.e. set the CO2 level to 0% on your incubator) and then try growing the cells in varying levels of CO2 (say 1%, 1.5%, 2% upto 5%).
You can start with a simple proliferation assay and also visualize the morphology of the cells in the above mentioned conditions. Then find out key proteins involved in the respiratory cycles and stress pathways and assess their modulation by the differing CO2 levels. Finally go further downstream to check changes in chromatin remodeling and gene expression.