Question: Help Needed About Snp And Genomic Co-Ordinates.
0
gravatar for Newtogenetics
7.6 years ago by
Newtogenetics0 wrote:

I am new to genetics research so please bear with me if my question is very trivial. I am trying to find information about SNPs for the gene coding thiosulphate sulphurtransferase (TST). My search on OMIM database shows the genomic co-ordinates only. When I checked the SNP database for TST in humans I found 183 rs numbers. How do I determine which SNP is the correct one? Is there any way that I can use the genomic co-ordinate to identify the correct SNP? Thank you.

sequence dbsnp snp genomics • 1.5k views
ADD COMMENTlink written 7.6 years ago by Newtogenetics0

Do you have the co-ordinates for the SNP or the gene?

ADD REPLYlink written 7.6 years ago by K_Star110
2
gravatar for Jorge Amigo
7.6 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

a single SNP may be responsible for a particular trait in some cases, but in some others several SNPs even several genes may be involved. when you search for SNPs on certain gene, you will get all the variant sites known to date, not exactly a particular and specific answer to your question.

ADD COMMENTlink written 7.6 years ago by Jorge Amigo11k

Right. It seems that all 183 snps of TST are your starting point. Try to filter out some of them. For example start looking only at tagging SNP (haploview do this for you) or snp reported in the GWAS catoalog (@ genome.gov). Then search literature....

ADD REPLYlink written 7.6 years ago by ff.cc.cc1.3k
1
gravatar for Karl
7.6 years ago by
Karl310
USA
Karl310 wrote:

A SNP is just a single nucleotide change. A gene could carry a thousand of them, and the regions nearby a gene could carry a thousand more that also play a role.

Usually we define SNP with some threshold of population abundance. If your whole population shares the same allele at a site, that SNP is pointless to study. Similarly if no one carries the mutation. For that reason a SNP is usually required to have more than 1% frequency in a population, and then there will still be a few or a dozen in every gene.

If you're looking for gene sequences that are distinct, then you need all the combinations of SNPs within the gene.

You have the tag dbSnp listed here, did you try looking up that reference? After you have the location of the TST gene (UCSC Genome browser can help there), then look at dbSNP for the known SNPs in the region.

ADD COMMENTlink written 7.6 years ago by Karl310
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