Get hg19 coordinates of SNPs from gwas catalog

Question

[MT]

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!

Answer 1

[Emily]

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.

Answer 2

[Jack]

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