The variants in the credible set for each locus, were annotated based on external reference data in order to evaluate potential functional consequences. In particular, we identify: (a) Gene and regulatory consequences annotated by Variant Effect Predictor (VEP) using Ensembl with genome build GRCh37124. We exclude upstream and downstream consequences, and consequences for transcripts that lack a HGNC gene symbol (e.g. vega genes). (b) Variants within 2kb upstream of the transcription start site (TSS) of at least one gene isoform based on Gencode v19125. (c) Variants annotated as interacting with a given gene in Hi-C data from samples of developing human cerebral cortex during neurogenesis and migration126. Annotations are considered for both the germinal zone (GZ), primarily consisting of actively dividing neural progenitors, and the cortical and subcortical plate (CP), primarily consisting of post-mitotic neurons. (d) Variants identified as eQTLs based on gene expression in GTEx127 or BIOS79. Expression quantitative trait loci were annotated using FUMA (see URLs). We restricted to eQTL associations with false discovery fate (FDR) < 1e-3 within each dataset. (e) Chromatin states of each variant based
