Get hg19 coordinates of SNPs from gwas catalog
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!
2 answers
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.
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