Schematic of the MAPT region and associated polymorphisms. Previous studies have identified a ~970 kb inversion polymorphism at chromosome 17q21.31, a region that contains MAPT and several other genes. Chromosomes with the inverted segment in different orientations represent two highly divergent MAPT haplotypes, H1 (direct orientation) and H2 (inverted orientation). No recombination has been identified between these two haplotypes over a region of ~1.5 Mb, but they have accumulated sequence variation independently. Polymorphisms including rs242562 and rs2435207 spanning MAPT exons 1 to 4 are specific to the H1 haplotype. Besides, there is a characteristic 238-bp deletion in the MAPT intron 9 of the H2 haplotype.