Question: Get hg19 coordinates of SNPs from gwas catalog
0
gravatar for MT
4.8 years ago by
MT20
European Union
MT20 wrote:

I have obtained a list of ~1000 SNPs from GWAS catalog, i.e:

rs6856616
rs10947261
rs751728
rs2149085
rs11195128
rs11235667
rs9271366

For which I need the genomic position. 

The GWAS catalog website states:

"The SNP data in the catalog has been mapped to dbSNP Build 141 and Genome Assembly, GRCh38/hg38."

However, dbSNP build 141 should be mapped to both hg19 and hg38.

What's an easy way to retrieve the hg19 position of the SNPs in question? Preferably using R or a web GUI.

 

Thanks!

hg19 gwas catalog • 4.2k views
ADD COMMENTlink modified 2.8 years ago by Jack110 • written 4.8 years ago by MT20
2
gravatar for Emily_Ensembl
4.8 years ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

Easiest way is Ensembl BioMart. There's a help video on using BioMart here. You'll want to use BioMart on our dedicated GRCh37 site here. Filter by your list of IDs, get IDs and locations as attributes.

ADD COMMENTlink written 4.8 years ago by Emily_Ensembl19k
0
gravatar for Jack
2.8 years ago by
Jack110
Jack110 wrote:

have a look at this . at least for my project, I found what I needed.

ADD COMMENTlink written 2.8 years ago by Jack110
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