Direction of effect

[basel-maher]

Does the direction of effect of a SNP in a GWAS affect colocalization? That is to say, does it matter if the provided z-score is positive or negative?

Thanks

[xqwen]

In brief, no. The colocalization analysis, in general, only cares if the underlying genetic effects are non-zero. The magnitude of the actual non-zero effects is implicitly integrated out.