Fine-mapping candidate neuropsychiatric regulatory variants using cell type-aware comparative genomics

Measures of nucleotide sequence conservation across species are useful for identifying functional genomic loci, but can fail when regulatory function is maintained, often in a cell type-specific manner, even when sequence is not. We introduce CTACIT, the Cell Type-Aware Conservation Inference Toolkit, to identify trait-associated regulatory variants. CTACIT integrates sequence conservation scores with cell type-specific open chromatin data collected from a few mammalian species to impute function for hundreds more. Applying CTACIT to neuropsychiatric trait loci identifies higher heritability enrichment and more fine-mapped variants than nucleotide conservation and human chromatin data alone. Our in vivo reporter assays validate predictions for enhancers with risk variants near the DRD2 schizophrenia risk locus. By integrating genome conservation and multi-species open chromatin data, CTACIT prioritizes variants within regions of conserved regulatory function for in vivo characterization and addresses a major challenge in translating disease associations to mechanistic understanding.