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Download SNPs data

I want to download SNPs data that contains every SNP's genotype with its magnitude, orientation and summary in a csv file or something like that.. for example:

rs4988235,minus,(C;C),2.5,likely to be lactose intolerant as an adult

is there is something like that available to download ?

snp genotype phenotype data

Have you tried BioMart at Ensembl?

I also want this for a personal project. Looks like I'm not the only programmer with personal interest in genomics.

I don't believe this type of information exists in a single file. You may have to merge it from dbSNP and the more clinically-related ClinVar files.

For dbSNP, this may help: List Of Dbsnp Rsids And Their Positions

The human dbSNP data is available for download here: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606 (you should devote some time to exploring that data, e.g., download different parts and see if t's what you could use).

Did you find out how to do it? I'm looking for THE EXACT SAME THING. Could you send me an email?

See @Emily's answer below. The link should work now.

Here is a direct link to the relevant VCF file (largeish download).

1 answer

Ensembl have VCFs of all phenotype-associated variants.

That indeed looks like the best fit to the user's question. I wasn't even aware of these VCFs by your organisation.

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