MAGMA LD reference panels
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Jamee Berg
Apr 17, 2026, 10:37:26 AM (4 days ago) Apr 17
to FUMA GWAS users
Hello!
I downloaded your MAGMA African reference panel (The reference data files are created from Phase 3 of 1,000 Genomes. The SNP locations in the data are in reference to human genome Build 37) and explored the .bim file.
I noticed that there variant_IDs (build 37), but no rsIDs:
My GWAS summary statistics only contain rsIDs
1)How is MAGMA using this reference panel if my GWAS sum stats only contain rsIDs.
2) Do you have a version of the MAGMA African reference panel that has rsIDs and not variant IDs?
Thank you!
I noticed that there variant_IDs (build 37), but no rsIDs:
My GWAS summary statistics only contain rsIDs
1)How is MAGMA using this reference panel if my GWAS sum stats only contain rsIDs.
2) Do you have a version of the MAGMA African reference panel that has rsIDs and not variant IDs?
Thank you!
Jamee
Tanya Phung
Apr 17, 2026, 3:37:16 PM (4 days ago) Apr 17
to FUMA GWAS users
Hi Jamee,
1. In SNP2GENE, when you submit a file with just rsID, FUMA extract chromosome and position from dbSNP v146:
1. In SNP2GENE, when you submit a file with just rsID, FUMA extract chromosome and position from dbSNP v146:
2. On the MAGMA website, the reference included there has rsID: https://cncr.nl/research/magma/. Note that this is not however available via FUMA.
Best,
Tanya
Tanya
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