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. 2022 Aug 18;54(9):1355–1363. doi: 10.1038/s41588-022-01154-4

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 9 — a) The top track shows −log10(p-values) of SNPs from the schizophrenia GWAS. The second and third tracks show −log10(p-values) from the THISTLE sQTL and eQTL analyses, respectively. The THISTLE sQTL and eQTL p-values were computed using a one-sided sum of chi-squared test and chi-squared test, respectively. b) Association of rs7198594 (the lead eQTL SNP) with the overall mRNA abundance of SETD6 in the ROSMAP data (n = 832). Each boxplot shows the distribution of mRNA abundances in a genotype class, that is, CC (n = 288), CT (n = 392), or TT (n = 152). The line inside each box indicates the median value, notches indicate the 95% CI, the central box indicates the IQR, whiskers indicate data up to 1.5 times the IQR, and outliers are shown as separate dots. c) Isoform-eQTL effects for SETD6 in the whole dataset (n = 2,865), with ENST00000310682.6 and ENST00000219315.9 at the two extremes with opposite isoform-eQTL effects. Each dot represents an estimate of isoform-eQTL effect with an error bar indicating the 95% CI of the estimate.