variable regions within exons of a gene
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4.4 years ago
genya35 ▴ 40

Hello,

Could someone please suggest where to find a list of variable regions (snps) within exons of a specific human gene located on chromosome six? I can locate the gene in ncbi and Ensemble but I'm not sure how to locate the SNPs. Which tools databases would be appropriate?

Thank you very much for your help in advance.

gene • 763 views
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4.4 years ago

You can have a look at ExAC and gnomAD

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4.4 years ago
Denise CS ★ 5.2k

For a list of SNPs on chr6 you can use BioMart. Choose Ensembl Variation 89 (as database), Human Short Variants (as dataset), chromosome 6 (under filters) and Variant name (under attributes). Ensembl 89 has > 9,000,000 short variants (e.g. SNPs) on chr 6 so you may want to do the query in batches or programmatically. This information will be available on the Ensembl FTP as well for Variation data.

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