finding directly the snp ids for the variants of each gene

Question

[jananiinfo14]

How to find directly the snp ids for the variants of each gene? thanks in advance

[WouterDeCoster]

Hello jananiinfo14!

We believe that this post does not fit the main topic of this site.

Insufficient information to get an answer, elaborate if you want help.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[Emily]

I think that's a little unfair. Yes, this is a naive question, but many people starting out their bioinformatics analyses are very naive and lack support in this area in their home institutes. We may be their only support.

(Also, it's an opportunity for me to suggest a newbie tries Ensembl. Not self-interested at all.)

[WouterDeCoster]

That's a valid point and concern, and definitely, we should stay supportive of those people. But in addition to being naive, this type of questions is also often a big waste of time when we try to drill down to find out what the OP truly wants to know. My first interpretation was that the OP has a vcf file and wants to annotate these with dbSNP id's, but your answer is also a possibility. With just a bit more effort on the side of the OP, this could be far easier and save a ton of effort for the community.

[Emily]

In that case I would comment with a question, but I wouldn't close it. When you close it you're really shutting down the conversation and making the OP feel like they can't ask naive questions, just asking a question invites them to engage.

[WouterDeCoster]

You are right - I will be more patient. I'm glad that moderatorship here is an itself-correcting system.

Answer 1

[Emily]

An easy way to do this is with Ensembl. Search for your gene name then go to Variant Table in the left hand menu to get a list of all the variants in the gene.

Answer 2

[Pierre Lindenbaum]

using UCSC/mysql:

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg19 -e 'select distinct S.name,R.name2 from snp150 as S, refGene as R where R.chrom=S.chrom and NOT(S.chromEnd<=R.txStart OR S.chromStart>=R.txEnd) and R.name2="NOTCH2" '
+-------------+--------+
| name        | name2  |
+-------------+--------+
| rs782287146 | NOTCH2 |
| rs150344945 | NOTCH2 |
| rs782430685 | NOTCH2 |
| rs191431654 | NOTCH2 |
| rs759289101 | NOTCH2 |
| rs868973669 | NOTCH2 |
| rs782330458 | NOTCH2 |
| rs782630792 | NOTCH2 |
| rs782609720 | NOTCH2 |
| rs2453056   | NOTCH2 |
(...)