enhancer3D is the first publicly accessible database of 3D chromatin models for archaic human genomes (Neanderthal and Denisovan), alongside modern human genomes.

It provides ensembles of full-chromosome and region-specific chromatin structures, generated using ChIA-PET interaction data and modified in silico with archaic structural variants (SVs). The database enables comparison of enhancer–promoter spatial distances and gene regulatory architecture across evolutionary lineages.