Shorter stature has been phenotypically linked to increased prevalence of schizophrenia (SCZ). Using genome-wide genetic data, we studied the SCZ-height relationship on a genetic level. We identified 22 independent lead SNPs (55% sign-concordant) and 142 genes statistically associated with both SCZ and height. Additionally, we found gene enrichment for pituitary cell-types and immune response gene-sets. While the global SCZ-height genetic correlation was nonsignificant, 9 genomic regions showed robust local genetic correlations (7 negative, 6 in the MHC-region). The shared genetic signal for SCZ and height within the 6 MHC-regions was found to be partially explained by mutual genetic overlap with serum white blood cell count, particularly lymphocytes. Fine-mapping prioritized 3 shared effector-genes (GIGYF2, HLA-C, and LIN28B) involved in immune response and developmental timing. Overall, the results illuminate the genetic processes involved in the SCZ-height relationship and illustrates the utility of genetic data in furthering epidemiological insight.

C.d.L is funded by Hoffman-La Roche. The other authors declare no competing interests.

C.R., D.P. and S.v.d.S were funded by NWO Gravitation: BRAINSCAPES: A Roadmap from Neurogenetics to Neurobiology (grant no. 024.004.012 [to D.P.]). D.P. and C.d.L. were funded a European Research Council advanced grant (no. ERC-2018-AdG GWAS2FUNC 834057 [to D.P.]). M.P.v.d.H. is supported by NWO VIDI Grant 452-16-015 and the ERC Consolidator of the European Research Council Grant 101001062. The analyses were carried out on the Genetic Cluster Computer, which is financed by the Netherlands Scientific Organization (NWO: 480-05-003), by the VU University, Amsterdam, the Netherlands, and by the Dutch Brain Foundation, and is hosted by the Dutch National Computing and Networking Services SurfSARA. This research has been conducted using the UK Biobank resource under application number 16406.

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All data produced are available online. Genome-wide summary statistics on SCZ GWAS Summary statistics can be downloaded from https://pgc.unc.edu/for-researchers/download-results/ and height from the GIANT consortium can be obtained from https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files. All other details on how to acquire data used in the present study are described in the data availability statement and additional links are provided in supplementary table 13.