Fig. 3

Prediction and functional characterization of target genes regulated by baaSNPs.A A circular diagram illustrates 53 candidate target genes predicted to be regulated by SNPs exhibiting biased allelic enhancer activity (baaSNPs) across four cell lines, based on expression quantitative trait loci (eQTL) analysis. The p-values shown are derived from the eQTL study. B Bar graphs display the most significantly enriched biological pathways among these potential target genes across the four cell lines, highlighting key neurological processes. C Chromatin loop data from neurons at three different developmental stages were utilized to map baaSNPs to their target genes, providing spatial context for gene regulation. D A Venn diagram depicts the overlap between genes associated with baaSNPs through eQTL analysis and those identified via Hi-C chromatin interaction data, indicating distinct but complementary sets of genes. E Results from a dual-luciferase reporter assay demonstrate the biased allelic enhancer activity of SNP rs3088186, confirming its functional impact. Bars represent the mean ± SEM. F An example locus of the MSRA gene illustrates that the baaSNP rs3088186 physically interacts with the MSRA promoter in neural progenitors (germinal zone), immature neurons (cortical plate), and adult neurons. Epigenetic annotation data were obtained from the UCSC Genome Browser.