1000 Genome Project - Synonyms Snps

Question

[Maxime Lamontagne]

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)

Answer 1

[Sean Davis]

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/

[Maxime Lamontagne]

Sorry, I forgot to talk about rs16960063.

Answer 2

[Laura]

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

[Maxime Lamontagne]

Thank you Laura.