GWAS lead variants- Which GWAS lead variants are linked with this variant?


When I explore variant page like this one Open Targets Genetics
I usually see in the “GWAS lead variants” table rows that belongs to the exactly same study with the same pubmed ID (I marked in red) that have diffrent study ids generated by open target genetics and their cohort size usually is different. If I click on Open target genetic study id, the “Independently-associated loci” numbers are different while this is bascially same study. My initial guess is that Open Target Genetics re-analyse these papers and keeps both original and re-analysed results in the portal. But even if that is the case why the case numbers are different? It is the same study with same cohort size.

Thanks in advance,


Hi Amir,

The rows you highlighted belongs to different studies, although they were both reported in the same publications. See, they have different study identifiers:

  • GCST90018741: LDL cholesterol association on 72,866 East Asian ancestry individuals.
  • GCST90018961: LDL cholesterol association on 343,621 European ancestry individuals, 72,866 East Asian ancestry individuals

So authors were repeating the associations using different sample stratifications. Sometimes these different approaches yield new associations, sometimes not. It worth following the study links to get more study level metadata on the conditions.

I hope I could make things clearer.


This explains it well. Which means it is always the best practice to use OTG study ids over pubmed ids, as the paper can be meta-analysis paper or as described might analyse different cohorts at the same time.

Many thanks!


Yes, there can be a number of reason why a publication is reporting multiple studies, most frequently associations for a number of traits are reported for example this publication reports 17 different hematological measurements, but also the studied individuals might be stratified by different variables eg. ancestry.

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