To evaluate the impact of alcohol treatment on the ASE of endogenous SNPs, we examined their expression in SK-N-BE(2) cells before and after treatment with two concentrations of ethanol, 10 and 20 mM. Among the 130 PASSPORT-seq SNPs showing ASE in SK-N-BE(2) cells, 17 had an average read depth per sample >15 and had at least 10% of their reads supporting the minor allele in either the ethanol-treated or untreated SK-N-BE(2) cells. Of these, we identified six SNPs whose ratios between reference and alternative alleles were significantly altered by alcohol treatment in a dose-responsive manner: rs45474901 (p = 0.014), rs2950846 (p = 0.017), rs45522239 (p = 0.022), rs45548238 (p = 0.027), rs1968676 (p = 0.029), and rs2338530 (p = 0.041). Three of these SNPs are located in the 3′UTR of TMEM25 (transmembrane protein 25), two are within PCDHB16 (protocadherin beta 16), and one is in SMPD4 (sphingomyelin phosphodiesterase 4). The SNP with the smallest p-value in each gene is shown in Fig. 4 (the other three SNPs are shown in Supplementary Fig. 4). For five of these six SNPs, the
