The model assumes that that there is no systematic correlation between FST and LD Score (see Supplementary Note). This assumption may be violated in practice as a result of linked selection (i.e., positive selection10 and background selection11). If there were a positive correlation between LD Score and FST , the LD Score regression intercept would underestimate the contribution of population stratification to the inflation in χ2statistics. To quantify the bias that this might introduce into the LD Score regression intercept, we performed a series of simulations with real population stratification.
