Independently associated SNPs do not translate to well-bounded chromosomal regions. Nevertheless, it is useful to define physical boundaries for the SNP associations to identify candidate risk genes. We defined an associated locus as the physical region containing all SNPs correlated at r2 > 0.6 with each of the 128 index SNPs. Associated loci within 250 kb of each other were merged. This resulted in 108 physically distinct associated loci, 83 of which have not been previously implicated in schizophrenia and therefore harbour potential novel biological insights into disease aetiology (Supplementary Table 3; regional plots in Supplementary Figure 1). The significant regions include all but 5 loci previously reported as genome-wide significant in large samples (Supplementary Table 3).
