The QTL Zoo

This document aims to provide a reference of the many types of QTL (Quantative Trait Loci) that are used in the literature:

• eQTL: expression QTL
• caQTL: chromatin accesibility QTL
• pQTL: protein QTL
• csQTL: cell state QTL ¹
• csaQTL: cell state abundance QTL ²
• int-eQTL: disease-state interaction eQTL ³
• mQTL: methylation QTL
• mQTL/metQTL: metabolite QTL
• haQTL: histone acetylation QTL
• miQTL: microRNA QTL
• fpQTL: footprint QTL ⁴
• n-eQTL: nuclear eQTL ⁵
• c-eQTL: cellular eQTL ⁵
• pcQTL: cis-principal component eQTL ⁶

References

Footnotes

1. Kluzer, A., Marioni, J. C. & Morgan, M. D. Milo2.0 unlocks population genetic analyses of cell state abundance using a count-based mixed model. 2023.11.08.566176 Preprint at https://doi.org/10.1101/2023.11.08.566176 (2023). ↩

2. Rumker, L. et al. Identifying genetic variants that influence the abundance of cell states in single-cell data. 2023.11.13.566919 Preprint at https://doi.org/10.1101/2023.11.13.566919 (2023). ↩

3. Natri, H. M. et al. Cell type-specific and disease-associated eQTL in the human lung. 2023.03.17.533161 Preprint at https://doi.org/10.1101/2023.03.17.533161 (2023). ↩

4. Dude, F. M. et al. Characterization of non-coding variants associated with transcription factor binding through ATAC-seq-defined footprint QTLs in liver. Preprint at https://doi.org/10.1101/2024.09.24.614730 (2024). ↩

5. Sakaue, S. et al. Early and late RNA eQTL are driven by different genetic mechanisms. Preprint at https://doi.org/10.1101/2025.02.24.639351 (2025) ↩ ↩²

6. Lawrence, K. et al. Focus on single gene effects limits discovery and interpretation of complex trait-associated variants. Preprint at https://doi.org/10.1101/2025.06.06.658175 (2025) ↩