Intra-European differences in LD Score can be a source of bias in the LD Score regression intercept. For instance, if one attempts to perform LD Score regression using the 1000 Genomes European LD Score on a GWAS with all samples from Finland, then the LD Score regression intercept may be biased upwards. Similarly, if one attempts to perform LD Score regression using the 1000 Genomes European LD Score on a GWAS with all samples from Italy, the LD Score regression intercept may be biased downwards. If we make the approximation that the intra-European differences in LD Score can be described by an additive term plus 5% noise (i.e., if we assume that the FIN LD Score equals the pan-European LD Score plus seven, which is a worst-case scenario among linear relationships between the two LD Scores in terms of bias in the intercept), then the bias introduced into the LD Score regression intercept by using the pan-European LD Score to perform LD Score regression on a Finnish GWAS will be 7 multiplied by the slope of the LD Score regression
