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

[Fin Swimmer]

Hello Sarah,

great! Thanks a lot. Ensembl support is awesome.

fin swimmer

Am 2018-08-17 12:39, schrieb Sarah Hunt:
> Hi Fin,
> 
> Thanks for reporting this one. Variants are now highlighted in the
> upstream and downstream regions of genes on this view. They are not
> annotated as being upstream and downstream variants in the popups, but
> hopefully this is obvious from the other annotations in the table.
> 
> Best wishes,
> 
> Sarah
> 
> On 03/08/2018 05:23, Fin Swimmer wrote:
>> 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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