Humans show distinct traits from primate and ancient hominin ancestors. GWAS loci for diseases and brain, heart, skeletal phenotypes enrich in four evolutionary genomic regions. Regions include human-macaque epigenetic differences, human accelerated regions, ancient selective sweeps, Neanderthal-introgressed alleles. Pelvic width and limb proportions enrich in regions mirroring primate fossil morphology changes. Longitudinal fasciculus loci enrich in human-gained epigenetic elements since macaques. Visual cortex loci enrich in human accelerated regions. Thalamus proper loci enrich in Neanderthal-introgressed alleles. Enrichments imply language processing in recent epigenetic shifts. Decision-making links to human accelerated regions. Sensory signaling and motor control tie to Neanderthal alleles. Traits evolved at varying evolutionary depths.