HG18 coordinates of rs#

Question

[win]

Hi all, I have a list of rs# and I want HG18 coordinates for each one of them. Is there a tool/ utility that can list HG18 coordinates for rs#. Following are a few examples:

rs10010131
rs10046
rs1004819
rs10050860
rs10077785

Thanks in advance.

Answer 1

[Neilfws]

There sure is: tools include the UCSC Table Browser or GRCh37 BioMart.

correction: Ensembl 54 BioMart

For the latter choose the variation database and the short variation (SNPs/indels) dataset, then supply your IDs as a list.

Here's a sample query using your first rs# - click the "results" button to see output.

[win]

On BioMart, how to set HG18 as the version?

[Neilfws]

Same as GRCh37 (the link I gave) NCBI36, more or less. If you strictly want HG18, use UCSC.

EDIT: sorry I misread your question. HG18 corresponds to NCBI36 which is Ensembl build 54, so you want this BioMart archive.

[win]

HG18 on UCSC worked and I get the start and end position of the variants. since I need a single value is the correct position the end or the start?

[Neilfws]

UCSC database coordinates are zero-based, so add 1 to the start. Which for a single base SNP, gives the same value as the end.