I've been dealing with these data myself recently, and can confirm
the data in March were build 129. They put the build 130 data up in
As a side note, build 129 is known to be problematic, as there are
multiple RS numbers that map to the same location:
According to their help team, this problem has been resolved in build
Hervé Pagès wrote:
> Hi Lin,
> I'm cc'ing the BioC list so other users might benefit from this.
> Lin Tang wrote:
>> Dear Dr. Pages,
>> I am using R package SNPlocs.Hsapiens.dbSNP.20080617 currently, I
>> to check with you that whether this package corresponds to dbSNP
>> 129 ? Although from the release date of this R package which is
>> months after the release of dbSNP build 129, it is logical to be
>> want to have it confirmed from you. I?d appreciate your kind
>> this. Thanks!
> It's hard to tell.
> According to these pages:
> Build 129 was released in April 2008 (note that the exact dates
> 2 pages don't match).
> A similar research shows that Build 130 was released about 1 month
> So at the time I downloaded the ds_flat_ch*.flat files from here
> in order to build SNPlocs.Hsapiens.dbSNP.20080617 (that was in March
> 2009), I assume that these files were a dump from Build 129.
> Note that the files under
> can change at anytime (and today they are indeed different from what
> were back in March). It's a sad thing that the SNP team at NCBI
> provide permanent URLs for their past builds. And it doesn't help
> the ds_flat_ch*.flat files they provide don't contain any
> about the build that they're coming from.
> Anyway, in the future I'll put the Build information in the
> file of the SNPlocs packages.
> One last note. According to the SNP team at NCBI "Human SNPs in
> are mapping to NCBI build 36.3". That is, to our
> package. According to UCSC, hg18 is NCBI Build 36.1 but NCBI Build
> NCBI Build 36.3 are identical from a *sequence* point of view (I
> makes them different are the annotations provided by NCBI).
> This means that, if you are planning to inject
> in a genome, it only makes sense to do it with
> In the future we will put in place a mechanism to make this
> i.e. check that the injected stuff and the host are compatible.
>> Lin Tang, Ph.D.
>> Scientist , Informatics | Sequenom Inc.
>> T: 1 858 202 9106 | F: 1 858 202 9084 | E: ltang at sequenom.com
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James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618