A casual variant is a mutation or difference in the genome that actually causes the difference in expression. These are very difficult to find in Genome Wide Association Studies (GWAS), as there are many variants that are not necessarily relevant to the expression in question or to expression in general. These are especially difficult to find within non-coding segments of DNA (introns). Identification of casual variants is also called “fine mapping”.
Useful Resources
[Identification of casual genes for complex traits](casual-genes-for-complex-traits.pdf)❌