Question: Why Are Some 23Andme Snp Ids Prefixed With "I" Instead Of "Rs"?
2
gravatar for jeff.hammerbacher
7.5 years ago by
United States
jeff.hammerbacher110 wrote:

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 • 6.1k views
ADD COMMENTlink modified 5.9 years ago by Andrius Bubelis0 • written 7.5 years ago by jeff.hammerbacher110
7
gravatar for Alex Khomenko
7.5 years ago by
Alex Khomenko70 wrote:

"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.

ADD COMMENTlink written 7.5 years ago by Alex Khomenko70
1

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

ADD REPLYlink written 7.5 years ago by Neilfws48k

Why don't they add these to dbSNP?

ADD REPLYlink written 5.9 years ago by cdsouthan1.8k
1
gravatar for Charles Warden
6.6 years ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

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

ADD COMMENTlink written 6.6 years ago by Charles Warden7.8k
0
gravatar for Andrius Bubelis
5.9 years ago by
United States/Miami/FIU
Andrius Bubelis0 wrote:

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)

ADD COMMENTlink written 5.9 years ago by Andrius Bubelis0
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