[ensembl-dev] No variants shown gene up- and downstream

[Fin Swimmer]

Hello Sarah,

we often use this kind of view to have a quick check whether there are 
known variants under our primers. It's quite hard to say how far from 
the transcript we are looking, as this depends why we put there a primer 
(amplify a promotor, amplify the whole gene, ...). With the way it was 
before - highlighting variants for all sequence that is shown - we were 
happy.

Thanks.


fin swimmer

Am 2018-08-02 15:38, schrieb Sarah Hunt:
> Hi Fin,
> 
> Thanks for the example link. You are correct - the upstream and down
> stream variants are no longer shown here either. Did you find it
> useful to have them here? And how far from the transcript would you be
> looking?
> 
> Thanks,
> 
> Sarah
> 
> 
> On 02/08/2018 13:12, Fin Swimmer wrote:
>> Hello Sarah,
>> 
>> I didn't mean the variant table. What I meant was the sequence view 
>> under "Exons" for a specific transcript, e.g. 
>> http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000134086;r=3:10145464-10147765;t=ENST00000256474
>> 
>> Sorry, if this wasn't clear.
>> 
>> fin swimmer
>> 
>> Am 2018-08-02 11:36, schrieb Sarah Hunt:
>>> Hi Fin,
>>> 
>>> We are no longer reporting upstream and downstream variants on our
>>> gene pages for human. The table was becoming cumbersome to use since
>>> the number of variants greatly increased in density.
>>> 
>>> We have a new variant table available from our location pages. To
>>> access if from a gene page, select the 'Location' tab then select
>>> 'Variant table' from the menu on the left. From the initial table, 
>>> you
>>> can use the usual location navigation to move along the chromosome.
>>> Here's an example link:
>>> 
>>> http://www.ensembl.org/Homo_sapiens/Location/Variant/Table?db=core;g=ENSG00000158158;r=2:96760498-96760998 
>>> I'm sorry we neglected to announce this in the release blog.
>>> 
>>> Best wishes,
>>> 
>>> Sarah
>>> 
>>> On 02/08/2018 09:57, Fin Swimmer wrote:
>>>> Hello,
>>>> 
>>>> may it be, that with the new realease, variants that are located up- 
>>>> or downstream of my selected gene aren't shown anymore?
>>>> 
>>>> I've checked whether I have any fiters active. But I haven't.
>>>> 
>>>> fin swimmer
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