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Significance Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are among the most mutable regions of our genome but are frequently underascertained in studies of disease and evolution. Using long-read sequence data from apes and humans, we present a sequence-based evolutionary framework for ∼20,000 phased STRs and VNTRs. We identify 1,584 tandem repeats that are specifically expanded in human lineage. We show that VNTRs originate by short interspersed nuclear element–VNTR–Alu retrotransposition or accumulate near genes in subtelomeric regions. We identify associations with expanded tandem repeats and genes differentially spliced or expressed between human and chimpanzee brains. We identify 52 loci with long, uninterrupted repeats (≥40 pure tandem repeats) as candidates for genetically unstable regions associated with disease.

Human-specific tandem repeat expansion and differential gene expression during primate evolution