Single-cell eQTL mapping in the human pancreas reveals cell-type-specific regulatory variants masked in bulk studies

Expression quantitative trait loci (eQTL) studies link genetic variants to variation in gene expression, helping to interpret GWAS signals in functional terms. In the human pancreas, prior eQTL work has largely been conducted in bulk tissue or in isolated pancreatic islets, treating the organ as a relatively homogeneous entity. However, the pancreas comprises a diverse range of cell types — including alpha, beta, delta, acinar, and ductal cells — each with distinct gene expression programmes and physiological roles.

A preprint posted to bioRxiv on 29 September 2026 reports single-cell eQTL mapping performed separately within individual pancreatic cell populations, using single-cell RNA-sequencing data from human donors. The authors identify eQTLs that are either cell-type-specific or differ in effect direction between cell types, findings that were not detectable in bulk analyses. The study also seeks to implicate specific cell types of action for eQTLs that co-localise with GWAS loci for metabolic disorders, including type 2 diabetes.

The work adds to a growing body of single-cell regulatory genomics resources and highlights that bulk-tissue eQTL catalogues may systematically miss biologically important regulatory variation that is confined to minority cell populations. This is a preprint and has not yet been peer reviewed (bioRxiv doi: 10.64898/2026.09.23.753551).