How to find disease related SNPs?

[Iffy]

Hello

I m working on disease named Alopecia areata and have 2 question:

1) I want to search SNPs for this disease. I have searched genes and
thier SNPs on NCBI but it gives all snps related to that gene.

2) In liturature search I have found some snp locations but how can i
locate that snp on gene?



Can anyone help me in this matter?

[123 Bioinformatics]

HI,

 Did you get the   "rs" ( dbsnp id ) number from the Literature ? then you can search the dbsnp data base.

Jeevan

--

"The Horse is made ready for the day of battle. But victory rests with the
LORD ". Proverbs 21:31

[Iffy]

On Nov 5, 6:24 am, "123 Bioinformatics" <123.bioinformat...@gmail.com>
wrote:

> HI,
>
>  Did you get the   "rs" ( dbsnp id ) number from the Literature ? then you
> can search the dbsnp data base.
>
> Jeevan
>

==========================================================================

Hi

No i dont get "rs" number from liturature else it will be easy to find
that snp from NCBI data base ..... I got information like this:

Gene Name Information
MX1 ====> 9,959 bp from the transcription start site.
AIRE ====> Six SNPs: C-103T, C4144G, T5238C, G6528A,
T7215C & T11787C
PTPN22 ====> R620W (c.1858C>T)

[Saneth Samarakoon]

Hi

If you have genomic locations of SNPs and do not know the SNP IDs (rs number) you can use ensembl  genome browser to find SNP IDs.

     1. In ensembl genome browser select Homo sapiens from the dropdown search box and type the gene name/symbol in the search text box
     2. Select the correct gene from the result list
     3. Select genomic sequence link of the menu bar appear in the left hand side of the webpage
     4. Set "show variations = yes" and "line numbering" in the "markup options" section and update.
     5. All the SNPs are highlighted in the result genomic sequence and
     6. Check the interesting location (genomic location you found from your literature survey) of the sequence and select the SNP. Use the link to visit the "ensembl SNPview" of that SNP

Hope you'll be able to find what you want

Pubudu

[Iffy]

================================================================================

 

Thanks for your help

This information is helpful but I have another question ... I am working on 20 genes and through liturature survey I only found SNP information of 3 genes...How can I find disease related SNP of other genes?

I am unable to find more through liturature

[Iffy]

Thanks for your help

This information is very helpful but I have another question ... I am

working on 20 genes and through liturature survey I only found SNP
information of 3 genes...How can I find disease related SNP of other
genes?

I am unable to find more through liturature & database searching gives
all snps of that gene but I only want those SNPs which are related to
disease "Alopecia Areata"

[KrocKs]

Hey..i designed a tool that serves this purpose...happy, if any feed
ba

http://mozart.bio.neu.edu/cgi-bin/kranti/query_cSNP.cgi

Kranti