Is rs# of an SNP comparable between genome version or build?

Question

[Rashedul Islam]

Hi All,

I am working on public genotype data in opensnp. I found that different platform (e.g., 23andme, decodeme etc) uses different genome versions (e.g., GRCh37 or GRCh36) and therefore, I have found different chromosomal position for the same reference SNP (rs#) id. For few SNP ids, I checked in dbSNP that the genotype remains the same even though the genomic position is shifted from GRCh37 to GRCh38.

My question is that if I want to infer biology (SNP association to a phynotype) from those SNPs obtained form different platforms, do I need to convert genomic position from different genome versions to one version? Or, can I use rs# to call a particular genotype independent of genome version?

Thanks in advance!

Answer 1

[Brian Bushnell]

A SNP with the same rsid should have the same effect regardless of the genome build; the coordinates are just shifted. Of course, other things could change with the build as well, which could perhaps move the SNP from a real gene to a pseudogene. And sometimes a SNP in one build will be at a location that does not exist in another build. But the vast majority of changes are just different absolute coordinates.

[Rashedul Islam]

Thanks @Brain for the comment. I also found relevant information in NCBI documentation here that "Depending on the organism, the net result of the alterations in assemblies and annotations mentioned above is that a SNP may be in an exon (or more generally, located in a gene) in one build, but then locate to an intron or UTR (or intergenic DNA) in the next build if the exon (gene) is removed between build releases. Once an organismÕs genome assembly comes closer to its finishing point, like that of the human genome, its annotation (including its SNP functional classification) will become more stable."

[GenoMax]

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