How did you generate the PCA? What do you mean by "unpruned A and LD pruned B"? If you're using different filtering on your A and B populations that could be driving your association.
From experience I'd warn you to remember that these are associations/correlations and can mislead you. I had a beautiful PCA that separated populations 1 and 2, only to discover that it was driven by X and Y-linked genes because I had an overrepresentation of females in one population. So just be careful how much you infer from these data.