GWAS Catalog hits

[mikefra...@gmail.com]

Hello,

I have submitted a job with a setting of : Maximum distance between LD blocks to merge into a locus (< kb) = 1000

I was looking at the GWAS catalog section of the results and I expected SNPs from GWAS catalog within 1000 kb of my SNP's LD blocks to come up.

But this is not what happened.

What is the meaning of the GWAS catalog section in terms of distance from my inputted genomic risk loci?

Thank you,

Mike

[Kyoko Watanabe]

Hi Mike,

I am sorry for my slow response.

That option "Maximum distance between LD blocks to merge" is used to merge the LD blocks of each independent significant SNPs into a single locus.

But this does not change the LD block of each independent significant SNPs.

Any annotations in FUMA including GWAS catalog is performed for SNPs that are in LD with one of the independent significant SNPs (with > user-defined r2 threshold).

So, to get GWAS catalog annotations in FUMA output, the SNP has to be in LD with one of the independent significant SNPs.

Hope this makes sense.

Best,

Kyoko