free DATABASE FOR SNP's for diabetes mellitus 2

Question

[neilgupte7]

I wanted free downloadable database for snps related to diabetes mellitus 2, any link for the same will be appreciated tried finding out many sites they had seperate snp infos , but i need an all inclusive downloadable dataset !

[Denise CS]

In addition to BioMart and depending on which information exactly you are after for all these SNPs for T2D, you can try the Open Targets Platform.

We use SNPs from GWAS, and many other data sources, to link genes to diseases e.g. type II diabetes mellitus. These SNPs are known by us as evidence. This is an example of SNPs used as evidence for type II diabetes mellitus (SNPs located in gene PPARG).

If you want to get this information programmatically, you can try the Open Targets REST-API.

This is one example of a REST API call to download the first 100 results for SNPs from GWAS associated with T2D in .csv and their associations:

https://api.opentargets.io/v3/platform/public/evidence/filter?disease=EFO_0001360&datasource=gwas_catalog&format=csv&size=100

You can also get the entire set of evidence (e.g. SNPs) from our data download page.

[neilgupte7]

thanks alot for the reply .....The given site had all the information what I wanted,can continue my further work now

[h.mon]

Hi neilgupte7,

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Answer 1

[finswimmer]

Hello,

maybe this is not what you understand by "all inclusive", but you should try biomart.

Select "Ensembl Variation 93" as database and "Human Short Variants" as dataset.

Under "Filter" you will find "GENERAL VARIANT FILTERS" and there a list of phenotype. Select what ever you want (with CTRL+Mouse-Click you can select multiple entrys).

Under "Attributes" you can select what informations should be included in the output.

fin swimmer