Is it possible to have different SNP search result using rs number and genome coordinate?

Question

[jessada.thutkawkorapin]

I have one SNP that I want to study. It has rs number rs4821700 and genome coordinate 22:38120041.

First I searched this SNP using rs number, rs4821700. It gave me a correct ordinate and variation, which is "22:38120041 G / A". It also gave me the population frequencies which are 0.2651. It also said that "This variant falls on 4 transcripts in 2 genes"

• ENST00000406386
• ENST00000344404
• ENST00000455236
• ENST00000492485

Later on, I searched for this SNP using the coordinate, 22:38120041. The result said that "No variants found." and the coordinate can be found in two genes

• ENSG00000100101
• ENSG00000100106

I also looked into those four transcripts and two genes and I couldn't find anything with my coordinate in those lists.

So, what did I do wrong? Can anyone guide me if the search results I got are actually correct?

PS: my coordinate was based on genome build GRCh37

Answer 1

[Ram]

How did you search by co-ordinate? I am familiar with most operations in NCBI and UCSC Genome Browser, but ensembl is not my cup of tea :(

FWIW, UCSC genome browser shows Ensembl transcripts overlapping with the SNP rs4821700

Answer 2

[a.polo88]

Hello,

Your questions in my opinion is simple to answer perhaps. The problem so to say of ensembl is that the database comprise all the variant of all the transcripts associated with the genome. I think that your problem can be solved simple searching what of these transcripts is the original transcripts. what this means? that you can click on the transcript that have the same aa length of your protein. for example if your protein have 346 aa. you'll have the original transcripts of the same length.

I have searched for your snp id and my result is this

• http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=22:37723534-37724534;v=rs4821700;vdb=variation;vf=3872478

• http://www.ensembl.org/Homo_sapiens/Variation/Context?db=core;r=22:37723534-37724534;v=rs4821700;vdb=variation;vf=3872478

• http://grch37.ensembl.org/Homo_sapiens/Variation/Context?db=core;r=22:38119541-38120541;v=rs4821700;vdb=variation;vf=3699077

• http://grch37.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=22:38119541-38120541;v=rs4821700;vdb=variation;vf=3699077

(Sorry the previous links were for GrCh38)

This is the map of variation in which you can search the location

I hope that the links are useful

• ENSG00000100106
• ENST00000344404

I think that your references are these

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs4821700

If you have any question I'm here

[Ram]

Hi a.polo88,I just stitched together all your answers into one. Feel free to edit and reshape it as you see fit!

[a.polo88]

thanks it is good