We annotated the 25 variants that showed ASE in the same direction in both SH-SY5Y and SK-N-BE(2) cells (Table 1). Eighteen were found to be in eQTL regions of their own genes, based on the GTEx database [22], which provides additional evidence that the identified genes are, at least in part, regulated by the cis-acting variants. In addition, 14 SNPs coincided with the binding site of one or more RBPs. Interestingly, poly(A)-binding protein cytoplasmic 1 (PABPC1) was associated with the location of 11 SNPs, while ELAV-like RBP (ELAVL1) was associated with 7. TargetScan matching of miRNA seed sites at each variant location using PolymiRTS [27] found 10 SNPs that disrupt or introduce a miRNA-binding site. Four of these SNPs interfere with the seed sites of 13 miRNAs that are known to be expressed in brains (Table 1).Table 1Annotations for SNPs that showed significant and consistent impacts in both SH-SY5Y and SK-N-BE(2) cell lines by PASSPORT-seqRegionGeneSNPMAF (%)eQTLRBP bindingPotential miRNA targetBLAPEAK1rs1738182118YesmiR-3913-3paBLAPNPrs107937532YesCEHELQrs469308934YesPABPC1, ELAVL1CEKIF1Brs106582833YesIGF2BP1CEKIF1Brs153626245YesIGF2BP1CEPACRGLrs681225731YesELAVL1, PABPC1CEZNF625rs598167411NoNACLYPD5rs45256023NoNACPCDHB16rs233853010YesPABPC1NACPRLRrs17362724NoPABPC1NACSLC16A4rs1112018YesELAVL1, PABPC1miR-200b-3pb, miR-200c-3pa, miR-374c-5pa, miR-429c, miR-4330b, miR-510-5pa, miR-512-5pb, miR-655-3pb, miR-8084a, miR-3942-3pc, miR-506-5pc, miR-5100b, miR-6074a, miR-889-3pc, miR-892c-5paNACSMPD4rs1090956738YesIGF2BP1NACSYT9rs1073251048NomiR-3925-3pb, miR-136-5pc, miR-4695-3pa, miR-665a, miR-766-3pcSFCCA13rs461714845YesELAVL1,
