Fig. 8

Allele-specific expression analysis results and expression pattern of target genes. a–j Ten transcription factor (TF) binding–disrupting single-nucleotide polymorphisms (SNPs) showed significant (Binomial P < 0.001) allele-specific expression (allelic imbalance) in human brain tissues from the GTEx. For each SNP, the counts of the reference allele and the alternative allele are shown. Of note, reporter gene assays also support that different alleles at rs1801311 and rs16937 conferred significant differences in luciferase activity, further supporting the regulatory effect of rs1801311 and rs16937. k Expression pattern of target genes of the identified regulatory SNPs across different developmental stages. The target genes of the identified regulatory SNPs showed a significant higher expression level compared with background genes (P < 1.0 × 10⁻⁷ for gene set in Supplementary Table 5, and P < 5.0 × 10⁻⁷ for gene set in Supplementary Data 4). In addition, we also found that the expression level of the target genes was higher in prenatal stage compared with postnatal stage (P = 0.001 for gene set in Supplementary Table 5, and P = 0.008 for gene set in Supplementary Data 4). The gray line represents the expression level of the background genes, the pink line represents the expression level of target genes listed in Supplementary Table 5, and the light blue line represents the expression level of target genes listed in Supplementary Data 4. l Cell type-specific expression analysis of the target genes of the identified regulatory SNPs. Target genes with a specificity score >0.1 were extracted and the number of targets genes with a specificity score >0.1 were plotted. Of note, the pyramidal cells have the most number of target genes, suggesting that the expression of target genes were enriched in pyramidal cells. Source data are provided as a Source Data file