Of the 128 variants, 124 were successfully imputed. However, one of the 124 variants (an indel on chromosome 6) was monomorphic in the MTFS. To replace the monomorphic and remaining four variants, we used surrogate variants from 1000 Genomes phase 3 that were in high linkage disequilibrium with the missing variants but were still significantly associated with schizophrenia in the PGC results. We used rs281768 (association with schizophrenia in PGC: p = 3.47 × 10−14) as a surrogate for an indel on chromosome 2, position 200 825 237 (p = 1.78 × 10−14); rs3798869 (p = 1.15×10−9) for an indel on chromosome 6, position 84 280 274 (p = 8.57 × −10); and an indel on chromosome 22, position 39 987 024 (p = 8.91 × 10−11) for an indel on chromosome 22, position 39 987 017 (p = 2.20 × 10−11). Since two of the unimputed variants (indel at chromosome 10, position 104 957 618 and rs7907645; p = 1.04 × 10−13 and p = 5.82 × 10−11, respectively) were within the same locus and we do not have
