Annotation of variants in risk loci showed limited evidence of functionality (Table 4 and Supplementary Note 1). Most notably for the AFA top hit on chromosome 13, when testing for chromatin interactions using Hi-C data in neural progenitor cells, significant chromatin conformation interactions were observed between the risk region and a region ~1100 kb upstream harboring additional non-coding RNAs including LINC00458, hsa-mir-1297 and LINC00558 as well as a region approximately 820 kb downstream harboring the pseudogene HNF4GP1 (Supplementary Fig. 24). eQTL analyses did not show significant associations with gene expression. However, the lack of functional data for this region may be explained by the African ancestry specificity of the GWAS findings since databases available within the FUMA framework, including GTEx and BrainSpan for eQTL analyses, are predominantly based on European populations.
