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38 reviewsSUMMARYMost genetic loci linked to polygenic traits are in non-coding regions, with complex regulation and linkagedisequilibrium (LD), complicating causal variant and gene prioritization. We used multiplexed single-cellCRISPR interference and activation perturbations to investigate cis-regulatory element (CRE) and geneexpression relationships within tight LD in the endogenous chromatin context. We demonstrated the prevalence of multiple causality in perfect LD (pLD) for independent expression quantitative trait loci (eQTLs) anduncovered fine-grained genetic effects on gene expression within pLD, which are difficult to decipher usingtraditional eQTL fine-mapping or existing computational methods. We found that over one-third of the causalCREs lack classical epigenetic markers prior to perturbation, and we functionally validated one of thesehidden regulatory mechanisms. Leveraging Multiome single-cell epigenetic and sequence perturbations,we highlighted the regulatory plasticity of the human genome. Our study will guide the exploration of missingcausal mechanisms underlying molecular trait regulation and disease development.
