Basepair Postition Of 5-Httlpr Length Polymorphism (Build37/Hg19)

Question

[User 6167]

Dear all,

I need to locate the length polymorphism 5-HTTLPR in the promotor region of SERT (SLC6A4). However, I can not find the Build37/hg19 basepair position of this length polymorphism. I searched ensembl, ucsc and dbSNP, but they all give the location of all of SLC6A4. Supposedly, this is because “5-HTTLPR” is used as synonym for SLC6A4. Also using Google I could not find how to locate the length polymorphism 5-HTTLPR.

Vinkhuyzen et al (PMID: 21670732) do locate 5-HTTLPR at 25586631 in their supplementary materials, but this was in a previous Build. I tried to use the surrounding SNPs they give to locate 5-HTTLPR, but 6 of the nearest SNPs in Vinkhuyzen mark an area of 296-401 SNPs in 1000Genomes. So, this is no accurate way to locate 5-HTTLPR either.

My final question is short: how do I locate the length polymorphism 5-HTTLPR in Build37/hg19?

Many thanks in advance,

Wouter

Answer 1

[Larry_Parnell]

Load that previous build into a genome browser like UCSC and go to that position in the supp. file. Use the surrounding SNPs you collected to verify that you're in the right place. An alternate approach is to go back to an early (original) paper that describes this variant and the method to detect it. Often, this is PCR-based and you can recreate that PCR electronically.

Answer 2

[User 6167]

Dear,

Thank you very much for your answer.

A collegue of me had an additional solution. She searched the region in dbSNP and found that 5-HTTLPR is represented as rs4795541 (17-28564357). And the published variation in this case is named as g.28564359_28564360delGGinsAGATGCTGGGGGGGCTGCAGGGGGGATGCTGGGGGTGCAGGGG, which means a deletion-insertion of this sequences between base pairs 28564359 and 28564360 of the reference genome.

Maybe this could be of help to others trying to locate 5-HTTLPR.

Best regards,

Wouter