Inquiry regarding chromosome location and genome assembly difference in SNP2TFBS

[Deepak Shankar]

Respected SNP2TFBS Support Team,

                                I hope this email finds you well. I have been recently using this SNPTFBS platform for transcription factor binding site prediction and have a discrepancy in chromosome locations and reference genome assembly.  According to the latest genome assembly, GRCh38.p14, my target SNP is located at 51339082 location at chromosome 15. I need to predict the transcription factor binding sites for this specific location within the GRCh38.p14 chr15. Could you kindly clarify is there any option to access that genome assembly in your current website in order to predict TFBS on my target. I would be graceful for your guidance. Thankyou for your time and assistance. 

Sincerely, 

Deepak

[CCG EPFL]

Dear Deepak,

I'm not sure whether you have to worry at all. If I understand correctly, your SNP of interest is:

rs7176005

This SNP is located on chr15 at positions 51631529 in human genome assembly hg19  and at 51339082 in  hg38. However, the surrounding sequences are the same in both assemblies, only the coordinates change. For this SNP, SNP2TFBS reports:

Sorry, no TFBS affected by the submitted SNP (rs7176005) according to SNP2TFBS!!!

The result would be the same for hg38.

If you need to convert genomic coordinates from hg19 to hg38, you can used the liftOver tool from UCSC:

https://genome.ucsc.edu/cgi-bin/hgLiftOver

I hope this clarifies the issue. If not, please explain in more detail what was your initial question and  how exactly you were trying to use our resource to find the answer.

Philipp