question about API for SNPs
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6.3 years ago
ahm3dhany ▴ 10

Is there any API that i can send to it the rsID (e.g. rs4988235) and the API respond with the position (i.e. chromosome number and position of the nucleotide) and the effect related to this rsID (e.g. for Rs4988235, CC: likely to be lactose intolerant as an adult. CT: likely to be able to digest milk as an adult. TT: can digest milk.)

SNP API Genotype phenotype • 2.4k views
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6.3 years ago
Denise CS ★ 5.2k

Yes, there is the Ensembl REST APIs. Two endpoints I could think of to get the data you are after are GET variation/:species/:ID (mainly) and the GET vep/:species/id/:id, which gives the added value of the annotation of your variant by the VEP. Check a previous biostars post.

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the main problem is there is no phenotype (e.g. for Rs4988235, CC: likely to be lactose intolerant as an adult. CT: likely to be able to digest milk as an adult. TT: can digest milk.)

I want an API that give me something like this: (the screenshot is from SNPedia) enter image description here

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If you know PERL, you can use the Variation API and get the phenotype annotations. If you know R, biomaRt would be a good way to get the phenotype info as well.

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thanks for this info on Ensemble Restful apis

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6.3 years ago

The dbSNP database can be queried for location and chromosome by RS#. You can download the dbSNP annotation and run queries on it, or maybe find an online resource.

For phenotype, it's much harder to be certain. The ClinVar database is another you can download that has a lot of those annotations, but most SNPs will not have known function.

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the main problem is there is no phenotype (e.g. for Rs4988235, CC: likely to be lactose intolerant as an adult. CT: likely to be able to digest milk as an adult. TT: can digest milk.)

I want an API that give me something like this: (the screenshot is from SNPedia) enter image description here

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