Transcripts containing exon 4.1 were also observed in GTEx brain tissue samples, but relative to the liver samples, their frequencies were low (Supplementary Table 10). We observed the same pattern, whereby rs2273500-C carriers had reduced splicing to exon 4.1 and increased splicing to exon 4.2, but these differences were not statistically significant (P=0.30) likely owing to the limited statistical power with the lower split read counts. However, we were able to evaluate rs2273500 as an eQTL SNP reliably using CHRNA4 mRNA expression levels measured across 10 regions of physiologically normal human brains from 134 European-ancestry participants in the Brain eQTL Almanac.46, 58 At the transcript level (Supplementary Figure 4), we observed that rs2273500-C was associated with decreased CHRNA4 expression in intralobular white matter. In further evaluation of this brain region (Figure 3), we found that rs2273500-C was associated with decreased expression at CHRNA4 exons 2–6 (lowest P=0.00073).
