Functional variants included a missense variant rs12140153 within PATJ, a synonymous variant rs11078398 within RAI1, regulatory variants rs10800796 in the promoter region of LMOD1, and rs239323 in a CTCF-binding site in the gene POM121L2. Using the Oxford Brain Imaging Genetics (BIG) server41, we further observed the pleiotropic locus at rs13135092 (SLC39A8, previously associated with blood lipids, height, schizophrenia, and other traits42) to be significantly associated with bilateral putamen and striatum volume in the UK Biobank (P < 2.8 × 10−7; N = 9,707; Supplementary Fig. 10). Here, RAI1 is linked to schizophrenia.