Why Are Some 23Andme Snp Ids Prefixed With "I" Instead Of "Rs"?
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8.4 years ago

I understand that "rs" is short for Reference SNP. What does the "i" prefix mean, and where can I learn more about this namespace for SNPs?

mitochondria snp • 6.5k views
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7
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8.4 years ago

"i" prefixes are for SNPs that don't have rsids, so if 23andMe wants to assay them, they have to give them some kind of internal designation, which is what this "i"-number is. Unfortunately, that means these SNPs don't live in any kind of standard namespace. Internally, 23andMe maps the i-number to the reference flanking sequence, chromosome position, and anything else they need to know about the SNPs to put it on a chip (a lof of these SNPs come from the custom portion of the genotyping array) and interpret the data later. As far as I know, they don't make this data publicly available.

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Yes, it's an "internal ID". In this case, presumably "internal" to 23andMe.

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Why don't they add these to dbSNP?

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7.4 years ago

If you have a question about a specific variant, you can probably ask 23andMe tech support how to get a more standard ID. I mentioned this in one of my blogs and they provided the rsID for that particular internal ID:

https://twitter.com/23science/statuses/42282105576763392

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6.7 years ago

If it exists, you can find the RS number by looking up the chromosome position of the SNP. Position data can be downloaded from the latest table from ncbi.nlm.nih.gov/SNP/ table name: b141_SNPChrPosOnRef. If no exact match is found, you can sometimes identify SNPs from the flanking regions.
ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606/b141_SNPChrPosOnRef.bcp.gz (human)

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