Variant location

Question

[fatma.mokhtar]

Hi all,

I have analyzed some associations with a phenotype using the PMRA array. In the info file regarding the SNP, I had many SNPs at the same time upstream and downstream of genes. How is this possible? Is a SNP location not always at one position? Please find attached the screenshot of the example. Could someone help me understand this?

Kind regards, Fatma

[iraun]

Please consider copy/pasting the line instead of screenshoting (it is quite difficult to see the text of the image). The SNP is located in a specific genomic position, but the functional annotation of the given SNP is different depending on the gene you are looking at. For example, a SNP could take place upstream respect gene1, but downstream respect gene2. As you can see in your image, under "Associated_Gene" field, you have several gene IDs, and the SNP will have a specific functional annotation for each one of the listed genes.

[fatma.mokhtar]

Thank you! Please find the information of the associated gene:

ENST00000306072 // downstream // 133424 // Hs.459265 // ISG20 // 3669 // interferon stimulated exonuclease gene 20kDa /// ENST00000561358 // downstream // 7506 // --- // --- // --- // --- /// NM_013227 // upstream // 13536 // Hs.2159 // ACAN // 176 // aggrecan /// NR_130134 // downstream // 133563 // --- // --- // --- // ---

But this SNP has a specific rs-number (rs62023469). I thought that a SNP is always on one gene, so if I understand correctly, we are not only looking at a gene but also transcripts? Do you have any suggestions (articles) to understand this more?

[iraun]

Yes sorry that is correct, to be more precise, you will get one functional annotation per transcript. The SNP has a unique identifier (rs62023469 in this case), and is located in a specific place. However, multiple transcripts located nearby are affected by the SNP.

Answer 1

[Istvan Albert]

The same region may be upstream of one feature and downstream of another. Or it could be upstream of two features (on different strands) etc.

The concepts of upstream and downstream are quite nebulously defined; it usually means a certain distance say 1 or 5 kb, depending on the organism.