Not appearing SNP in region plot

[Ariadna Cilleros Portet]

Hi, 

I uploaded a GWAS and everything was working fine, but when I was having a look at the region plot, I noticed that one of my SNPs was not there. This SNP has been detected with its rs ID, as it appears in the tsv file that I can download from the "Download summary stats" option located on the main page. Does anyone have an idea of what is happening and how can I solve it? 

Thank you so much!

Ariadna

[Andrew Boughton]

It's hard to say what's happening without more context. Two scenarios where a variant might be hidden come to mind, but I'm not sure that either apply.

1. Some old GWAS programs output variants that are malformed in some way and cannot be handled. (Pvalue=0, parsing errors etc) This is usually noted in the ingest logs with the failure reason, and I wouldn't expect the variant the appear in the harmonized summ stats download in that case. 

2. For performance reasons, we sometimes do not render variants of very low significance if your plot has a huge number of data points.(multiple low significance dots are combined into one blob) Zooming in would often cause it to appear. However, I would be surprised if that was the answer here, because it would be almost beyond the limits of the human eye to pick out the dot under those conditions.

-Andy Boughton

abo...@umich.edu

On Jan 4, 2024, at 7:08 AM, Ariadna Cilleros Portet <ariadnac...@gmail.com> wrote:

Hi, 

I uploaded a GWAS and everything was working fine, but when I was having a look at the region plot, I noticed that one of my SNPs was not there. This SNP has been detected with its rs ID, as it appears in the tsv file that I can download from the "Download summary stats" option located on the main page. Does anyone have an idea of what is happening and how can I solve it? 

Thank you so much!

Ariadna

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[Ariadna Cilleros Portet]

Hi Andrew, 

Thank you so much for the quick answer. I have made public the GWAS on LocusZoom webpage (https://my.locuszoom.org/gwas/118775/) in case you could check it. The SNP that I am looking for is rs11637580 (15:67412038). I didn't experience any failure during the upload, therefore, as you said, I don't expect that this could be the problem. Regarding the other option, I have zoomed in, but it is not there... Its transformed p-value is 4.13. Anyways, do you think that there could be any other solution? 

Thank you so much in advance!

Best, 

Ariadna

El dia dijous, 4 de gener del 2024 a les 14:59:43 UTC+1, Andrew Boughton va escriure: