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The human genome is thought to contain 100s of thousands of enhancers with, as yet, uncharacterised activities and a large proportion of disease-causing and disease-predisposing DNA sequence variants map to potential enhancers. To advance understanding of human disease, massive efforts are currently being directed towards establishing genotype to phenotype correlations for sequence variants. A key pre-requisite to these analyses is defining the precise cell- and tissue-specific activities of the enhancers, in a context that is relevant to the biology associated disease.Our research focuses on addressing this knowledge gap by building in vivo and ex vivo models for visualising and defining cell-type specific enhancer functions using an exemplar locus for enhancer- mediated gene regulation- PAX6, the master regulator of eye development. PAX6 has a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive, redundant, or distinct functions is unknown.We have developed in vivo (zebrafish) and ex vivo (optic cup organoids) models enabling visualization of the precise spatial and temporal roles of PAX6 enhancers in the developing eye. Using a combination of high-resolution live imaging, single cell RNA- sequencing and synthetic biology approaches in these model systems we have uncovered cell type specific regulatory activities of enhancers at single-cell resolution. Here I will present our most recent work revealing enhancer usage dynamics during zebrafish embryonic development at cell-type specific resolution in a fully synthetic complete PAX6 regulatory domain integrated in the zebrafish genome.