How to find gene id and gene name after I know rsid

Question

[Phylicia]

As I asked, how to find gene name and gene id after I know the rsid?

I found previous post (Get gene names from rs SNP ids) is useful.

After I applied it, I found a lot of SNPs can not find gene id. I want to ask whether there is updated method.

Thank you very much.

[manaswwm]

Do you have any example SNP IDs for which you did not find a gene id? Maybe these are SNPs not occurring within the coding regions?

[Phylicia]

Thank you very much. It makes sense.

[LauferVA]

SNPs do not affect genes so much as they affect transcripts

there are numerous tools available online through more or less every major biological database. if it were me in your position, i'd start by looking into databases like ClinVar, Ensembl, dbSNP, dbGAP, UCSC table browser ... etc.

[Phylicia]

Thank you. I have tried use R code to look for gene name for a large group of SNPs which is more convenient. It will be good if I can use the code to do it for all the SNPs at the same time.

[LauferVA]

i recommend that you clarify what your goals are before going any further.

for example, you have said that some SNPs do not affect genes. this is of course true. but are you clear on why that is true? if not, i would stop what I am doing and first figure that out...

there are millions and millions and millions of SNPs out there. there are some reasons to want to download all of them, but ... not that many good reasons. again, what is your goal?

[Phylicia]

Thanks. My goal is to use a website software to do colocalization. It requires SNPs with gene id and gene name. Can you try to answer my other post asking LD matrix if you can help? Thank you very much.