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

[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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