Is there a ready list of all SNPs in UCSC?

Question

[m321.k321]

I have list of few thousands snps name (RS*) and want to know their MAF.

I used the link http://genome.ucsc.edu/cgi-bin/hgTables

But i get errors that not all the SNPs are known.

This is why first I want to check which SNP exist in UCSC.

How can I do it? Is there a list of all known snps in the UCSC.

If there is such list that I can download, I will make a short code in phyton to compare my SNPs.

Thanks

Answer 1

[Alex Reynolds]

Here's a one-liner to get a list of UCSC SNP names:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'SELECT name FROM snp138Common' | tail -n +2 > snp138CommonNames.txt

If you want positional data, etc. there are other fields available in the snp138common table schema.

For example, if you want to know the type of functional variant for a given SNP name, add the func field to the query:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'SELECT name, func FROM snp138Common' | tail -n +2 > snp138CommonNamesAndVariantTypes.txt

Answer 2

[Asaf]

In the table browser (the link you posted) choose: group:Variation -> track:all SNPs(138) and get the output, the fifth columns is the SNP name rs*.

[m321.k321]

Hi Asaf,

each time that i try to run this with all SNPs the chrome is crashing...

[Pierre Lindenbaum]

solution: don't use chrome.

Answer 3

[Emily]

Or, more easily, use Ensembl BioMart. Use the short variation database, filter by a list of IDs and get the MAF as an attribute. No coding involved.

Answer 4

[m321.k321]

Emily_Ensembl,

when you say "get the MAF as an attribute" - fo you mean the 1000 genomes global MAF (ALL)?

Because I understood that the UCSC is the most accurate database and the MAF there is the most accurate?

[Emily]

Yes, the 1000 genomes MAF will be good.

The dbSNP data in UCSC and Ensembl all comes from the same place - one possible difference is that Ensembl carry out an extensive QC process to get rid of anything that looks dodgy, whereas I believe UCSC lift it directly.

[m321.k321]

Thanks.

Can I get more info of the snp? like name of the gene or intergenic? inside intron or exon?

:)

[Emily]

Yep, that's all under Gene associated information.

[m321.k321]

I couldn't find gene name. can you help me to find this attribute? thanks

[Emily]

I'm afraid we don't have the associated gene name for variants. I'll speak to our team to see if we can get that added. In the meantime, you can get the ID then use the genes database to convert it.