Nine structural haplotypes segregate at 17q21.31. H1 harbors duplication β covering 300kb of KANSL1 at 26% in Europeans. H2 harbors duplication α covering 150kb of KANSL1 at 19% in Europeans. Both duplications absent or rare in 502 East Asian and 316 African chromosomes. Duplications produce novel truncated KANSL1 transcripts retaining coiled coil but lacking PEHE domain. Locus associates with female fertility, meiotic recombination, and neurological disease. H2 inversion positively selected in Europeans. Ancestral H2.α1 haplotype present in Central African Pygmies. Duplications show greater population differentiation than H2 inversion. Beta duplication arose 20-27kya with 12kya coalescence in Europeans. Alpha duplication older than 1Mya but coalesced 17kya in Europeans. Parallel frequency increases suggest selection on common phenotype like fertility. Structural haplotypes impute accurately from SNPs with r2 up to 0.99. Gamma duplication of NSF gene also varies multi-allelically. Complex structures reconstructible via population genetics without FISH or clones.