[ensembl-dev] Disappeared Variation synonyms

Ma, Man Chun John manchunjohn-ma at uiowa.edu
Wed Jun 27 17:17:18 BST 2012

Hi all,

V67's inclusion of dbSNP 136 updates for rat is clearly good news, as this bridged a gap between the two databases (many Ensembl rat SNPs were pulled from dbSNP post-130 and they were not re-included into dbSNP for the past 3 years).

However, when I attempted to access one of those SNPs I haven't been able to locate them using the previous ENSSNP IDs. After searching for the SNPs in question by using genomic coordinates, I've noticed the v67 entry included none of the synonyms listed in v66.

For example:

rs105805725 in v67 (http://www.ensembl.org/Rattus_norvegicus/Variation/Summary?db=core;r=17:39585392-39585392;source=dbSNP;v=rs105805725;vdb=variation;vf=5120020) vs rs65331131 aka ENSRNOSNP971187 in v66: (http://feb2012.archive.ensembl.org/Rattus_norvegicus/Variation/Summary?r=17:39584892-39585892;source=dbSNP;v=rs65331131;vdb=variation;vf=3051002). They are essentially the same Variation (same position and alleles and even individual genotypes), yet the v67 entry did not include any synonyms seen in v66.

Due to the issue mentioned in the beginning of the email, any rs# for these SNPs in pre-v67 are de jure invalid, and our lab relied on the ENSSNP ID for identification. I hope those ENSSNP IDs have not been retired so abruptly right?


John MC Ma
Graduate Assistant
Kwitek Lab
Department of Pharmacology
3125E MERF
375 Newton Road
Iowa City IA 52242

Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.

More information about the Dev mailing list