We performed cross-ancestry fine mapping to identify credible sets with 99% PIP for causal variants proximate to 92 independent lead variants in the cross-ancestry meta-analysis (Supplementary Tables 7 and 8). The median number of SNPs in the credible sets was nine. We found that 13 credible sets contain only a single variant with PIP ≥99%; 47 credible sets contain ≤5 variants (Fig. 2b). For example, fine mapping the region proximate to lead SNP rs12354219 (which maps to DYPD on chromosome 1) identified rs7531138 as the most likely potential causal variant (PIP of 48%), although this variant and rs12354219 (PIP of 11%) are in high linkage disequilibrium (LD) in different populations (r2 ranges from 0.76 to 0.99). In a cross-ancestry meta-analysis, rs7531138-T (the risk allele for PAU) was significantly positively associated with schizophrenia (P = 1.04 × 10−8), but rs12354219 (P = 6.18 × 10−8) was not significant30. Rs7531138-T was also associated with decreased EA (P = 1.74 × 10−11), and again, rs12354219 was not (P > 5 × 10−8)31.
