H1 and H2 haplotypes diverged 2.3 million years ago. H2' ancestral haplotype lacking duplications enriched in African hunter-gatherers like San, Hadza, Pygmies. H2 absent in West Africans, highest 13% in Sudanese Beja due to Middle Eastern admixture. H2D with short CNP155 duplication fixed in European H2, arose 1.3 million years ago in Africa. H1D with long CNP205 duplication arose 250,000 years ago, absent in Africans and Asians. 60% Europeans carry at least one duplication vs. near zero in Africans and Asians. H2D haplotypes show extreme low nucleotide diversity indicating recent bottleneck or selective sweep in Europeans. Europeans vastly overrepresented in 17q21.31 microdeletion cases causing intellectual disability. H2D only haplotype predisposing to NAHR-mediated microdeletion due to direct-oriented duplications. H2 protective against Parkinson's and other diseases but raises microdeletion risk. CNP210 NSF duplication highest in Asians, up to 8 copies exclusively Asian. Eight structural haplotypes identified, H2.1 simplest like great apes. Double recombination homogenized 30kbp CRHR1 region between H1 and H2 despite ancient split. H2 missense mutations in IMP5 predicted to alter protein, potentially under positive selection. Duplications increased KANSL1 expression linked to brain function and disease.