We identified 88 SNPs with ASE in at least one brain region that significantly differed between subjects with and without AUD (Fig. 2a) at an FDR < 0.05 and |β12| > 1. Among these SNPs, 58 showed an increased fraction of the alternative allele in AUD samples, while 32 showed a decreased fraction. There were 26 SNPs in the BLA, 9 in the CE, 31 in the NAC, and 22 in the SFC. Examples of SNPs with significant differential ASE in each brain region are shown in Fig. 2b. An annotated list of these 88 SNPs, including their loci, allele frequencies, gene, and functional location, is provided in Supplementary Table 3. In addition, we developed an R-shiny-based interactive website (https://yunlongliulab.shinyapps.io/aud_ase/) to provide a direct visualization of the ASE findings. This data portal exhibits the RNA-seq read counts on both reference and alternative alleles at each significant ASE locus for every subject.
