dbnSNP frequency anomalies
I'll stick my neck out and simply state that allopatry alone would account for the pattern you are observing. Thus populations can exihibit variation in allelic profiles, particularly where Mendellian inheritance is operating (i.e. higher eukaryotes), singly due to geographic isolation.
This represents the Meyers view of population genetics and would account for variation within neutral theory, e.g. silent mutations. Obviously I'm guessing the populations were selected by geographic foci in generating the allelic frequencies.