chr1swallace/coloc

How to interpret coloc.susie results with two different variants in low LD?

Closed this issue · 6 comments

wonjikim11 commented

Hi,

I visited #84 and figured out how to interpret coloc.susie results with two different variants in high LD.
In most cases, they were in high LD but some were in low LD such as r2=0.5, and I wonder how to interpret this.
Can I interpret this as multiple causal variants?

One more, if I found two colocalizations involving one eQTL and three variants, e.g.
eQTL1 - variant1 & variant2
eQTL1 - variant1 & variant3,
can it be considered one colocalization involving three variants?

Thanks!

chr1swallace commented
wonjikim11 commented
  1. They are in the same credible set.
  2. Let me take a look at the plot_dataset(). I used coloc.susie on gwas and eqtl with summary statistics. I wonder if multiple colocalizations sharing a causal variant can be interpreted as a single colocalization with multiple causal variants.
chr1swallace commented
wonjikim11 commented
  1. So, in what cases can we conclude that there are multiple causal variants? If they are in the different credible sets?
chr1swallace commented
wonjikim11 commented

I got it. Thank you!