How many 23andMe SNPs have rsIDs and Minor Alleles in dbSNP?
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7.1 years ago

How many 23andMe SNPs have rsIDs and Minor Alleles in dbSNP?

(Apologies if this has been answered before)

gene snp 23andMe rsID Minor Allele • 2.9k views
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Thanks matted. Is this ratio still the same since 23andMe dropped their number of SNPs to about 600,000? They no longer give 900,000 snps.

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I didn't know that changed.  My results are from 2011.  It looks like the other answer here addresses the more recent set.

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You all are awesome! Thank you so much.

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I've moved additional questions and comments that were posted as answers up here. If you like the answers, please upvote them and select one or more as best answers.

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Andrius Bubelis's answer works best but I'm on my phone and can't see the 'thumbs up' icon to 'up vote it'.

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7.1 years ago
matted 7.5k

Based on my quick look, it's almost all.  Assuming all recent 1000 Genomes SNPs are in dbSNP, I compared the genotypes in my 23andme data to the latest 1000 Genomes VCF file.  911436 of 966977 SNPs are present in the 1000 Genomes set.  The bulk of the "missing" ones are probably not autosomal, since the 1000 Genomes VCF I used only included autosomal data.  There are only 10249 23andme SNPs that don't have rsIDs.

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7.1 years ago

My 23andme test processed September 2, 2014:

23andme SNP TOTAL COUNT: 598897

with "rs" number: 552726

with "i" (without "rs") number:  46171

Interesting observations:

- 627 out of 552726 (with "rs" number) do NOT exits in dbSNP ( NOT IN (SELECT * FROM dbSNP..SNP)  )
), e.g.: rs16344,rs1793987,rs1799735,rs1800554,rs1818952,rs2032651,rs2073619,rs2189335,rs2228005,rs2251862

- I found that 1914 out of 46171 (without "rs" number) in dbSNP database match on chromosome and position (table dbSNP..b141_SNPChrPosOnRef)

dbSNP Build 141 (latest as of today - October 14, 2014)

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