through chromosome conformation analysis performed in tissue from the developing brain using Hi-C41 physical interactions (Methods and Supplementary Table 12). One of the implicated alleles was a nonsynonymous variant in the manganese and zinc transporter gene SLC39A8. Nonsynonymous variants in this gene, which lead to SLC39A8 deficiency, have been associated with severe neurodevelopmental disorders putatively through impaired manganese transport and glycosylation42, highlighting a mechanism of therapeutic potential for schizophrenia.