[ensembl-dev] Automate the SNP variant result from "population genetics"

[deepak kumar]

Dear ALL,

 I have been looking for a way to find "which nsSNP (with rs ID number like
rs769971095) belong to what population(s), and if possible what gender"? I
came to know about the Ensembl "population genetics" for the variants.

I found the respective population genetics info for 2 rsIDs; rs559632360 &
rs769971095

For "rs769971095" the super-population it shows is: ALL, AFR, AMR, ASJ,
EAS, FIN, NFE, OTH, SAS.

For "rs559632360" the super-population it shows is: ALL, AFR, AMR, EAS,
SAS, EUR.


For rs559632360 rsID, it also shows population genetics from "1000 Genomes
Project Phase 3 & gnomAD exomes" along with "subpopulation" information,
whereas, for rs769971095 it shows only "gnomAD exomes" population genetics.

http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:12625875-12626875;v=rs769971095;vdb=variation;vf=135759093

http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:12632759-12633759;v=rs559632360;vdb=variation;vf=92299087#population_freq_SAS

Does this mean that for "rs769971095" there is no "1000 genomes project
phase 3" data available?

I am interested to know if these two rsIDs belong to one population, so,
can it be said that these rsIDs share same population? If yes, what
population they share? It would be great if I could know how to make a
reasonable interpretation for this.

Also, I need to do this for many rsIDs, could you please let me know how
this process can be automated? Where, I can generate results like this:


*rsID                  Super-Population with allele frequencies
 Sub-population*

rs769971095     ALL, AFR, AMR, ASJ, EAS, FIN, NFE, OTH, SAS.      .......etc

rs559632360      ALL, AFR, AMR, EAS, SAS, EUR
 ......etc



Thanks much! DK
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