Question: 1000 Genome Project - Synonyms Snps
1
gravatar for Maxime Lamontagne
7.5 years ago by
Qu├ębec
Maxime Lamontagne2.1k wrote:

Hi everyone,

In the 1000 genome browser, for some snps you have synonyms. Very often, they are on the same chromosome and close to each other. I guess this is just a build problem.

But I found a snp (rs16960052) with a synonym snp on an other chromosome, with different allele frequency and different flanking sequence. Why this is happening?

(http://browser.1000genomes.org/Homo_sapiens/Variation/Summary?r=13:102976640-102977640;v=rs16960063;vdb=variation;vf=12220262)

Thaks, Maxime.

EDIT:

When your search for rs16960052 in 1000 genome browser, it give you another snp (rs16960063). When you look for this snp, it said they are synonyms but they are not on the same chromosome.

(http://browser.1000genomes.org/Homo_sapiens/Search/Results?site=ensembl&q=rs16960052)

genome snp • 2.1k views
ADD COMMENTlink modified 7.5 years ago by Laura1.7k • written 7.5 years ago by Maxime Lamontagne2.1k
3
gravatar for Sean Davis
7.5 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

SNPs with "rs" in front are dbSNP identifiers, so that is the database that you would generally want to look to for information. The SNP rs16960052 is the result of merging two different snps.

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs117139582 http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs58762263

If you have questions about dbSNP entries, I suggest that you contact dbSNP. Also, you might find the dbSNP FAQ useful.

http://www.ncbi.nlm.nih.gov/books/NBK3848/

ADD COMMENTlink written 7.5 years ago by Sean Davis25k

Sorry, I forgot to talk about rs16960063.

ADD REPLYlink written 7.5 years ago by Maxime Lamontagne2.1k
0
gravatar for Laura
7.5 years ago by
Laura1.7k
Cambridge UK
Laura1.7k wrote:

This is a bug in the version of ensembl (61) which sits behind our browser. This will be fixed when the next browser is released which is hopefully soon

thanks

ADD COMMENTlink written 7.5 years ago by Laura1.7k

Thank you Laura.

ADD REPLYlink written 7.5 years ago by Maxime Lamontagne2.1k
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