Genome-wide SNPs included five non-coding RNA exonic variants, one variant downstream of lincRNA AC107892 (ENSG00000266213) and one intergenic variant. In the GTEX data, AC107892 is expressed at low levels across brain tissue, particularly in the substantia nigra (Supplemental Figure 3). In the HUGIn database, interaction of rs12954372 was observed with LINC01029 in dorsolateral prefrontal cortex tissue (p<0.01) and SALL3 (p<0.001) in hippocampus tissue (Supplemental Figure 4), SALL3 in neural progenitor cells (p<0.00001), and ATP9B and MBP in embryonic stem cells (p<0.00001). HaploReg V4.1 indicated that rs12954372 alters regulatory motifs in some cell types, including H1 and H9 derived neuronal progenitor cells, in the ROADMAP Epigenomics data.
