Question: Two genes in one SNP
1
gravatar for first
5 weeks ago by
first30
first30 wrote:

I am wondering how to interpret the following sample data:

rs_number;gene
rs11980782;AGMO-MEOX2
rs1800497;ANKK1|DRD2

(semicolons used as column separator)

How is the relationship between the SNP and the gene described? Both cases has two different genes annotated for the particular rs number. Would the proper interpretation be that the SNP is located between the two or should it be within the two?

Also is there any way I could just choose which is my gene of interest and discard one of the two?

snp gene • 179 views
ADD COMMENTlink modified 4 weeks ago by zx87547.1k • written 5 weeks ago by first30

Check dbSNP (rs) versions. There seems to be some change between the versions. first

rs11980782

rs11980782

rs1800497

rs1800497

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by cpad011211k
2
gravatar for h.mon
5 weeks ago by
h.mon24k
Brazil
h.mon24k wrote:

I don't think there is an easy answer. The proper way to try to interpret is to search several sources of information and try to reach a conclusion. For example, just googling both SNP IDs will lead you to the SNPedia page for rs1800497, there you will find some pertinent information regarding your questions.

Another approach would be to search NCBI dbSNP for both SNPs, then explore the resulting pages. Here is the reference SNP page for rs11980782, and here is the page for rs1800497. There is plenty of information to help you clarify the relation between those SNPs and the associated genes.

ADD COMMENTlink written 5 weeks ago by h.mon24k
1
gravatar for pltbiotech_tkarthi
4 weeks ago by
CIMMYT, Mexico
pltbiotech_tkarthi170 wrote:

According to NCBI Gene search, these two genes physically located at adjacent regions in chromosome 11. Concerning TaqI assay for rs1800497;ANKK1|DRD2 for an allele, a SNP polymorphism was observed around 10000bp downstream of DRD2 (at downstream after CDS region of DRD2), where ANKK1 kinase gene also physically located on the downstream region of DRD2 . Both of them physically located around 133, 390-113,450 kb region at human chromosome 11. These two genes physically and genetically linked for certain disorders. So you have to consider both these genes for your study. Read this https://www.ncbi.nlm.nih.gov/pubmed/15146457. Additional info: https://www.ncbi.nlm.nih.gov/gene/?term=Taq1A, https://www.ncbi.nlm.nih.gov/gene/1813, https://www.ncbi.nlm.nih.gov/gene/255239 , https://www.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000170209;r=11:113387791-113400418

I think there may a linkage between AGMO/MEOX2 genes for rs11980782;AGMO-MEOX2 as well, please check it thoroughly.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by pltbiotech_tkarthi170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1116 users visited in the last hour