Download SNPs data

Question

[ahm3dhany]

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 ?

[GenoMax]

Have you tried BioMart at Ensembl?

[cjohnweb]

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

[Kevin Blighe]

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).

[Corentin]

You can also look at the R package "gwascat": https://bioconductor.org/packages/3.7/bioc/vignettes/gwascat/inst/doc/gwascat.pdf which allows you to access and work with the National Human Genome Research Institute GWAS catalog.

[Blake Young]

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

[GenoMax]

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

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

Answer 1

[Emily]

Ensembl have VCFs of all phenotype-associated variants.

[Kevin Blighe]

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