The same SNP in different region

Question

[fatma.mokhtar]

Hallo,

I have looked in a paper where they have found 2 SNPs (rs7534124 and rs1136774) in the promoter region, this article was ( Association between SNPs in the promoter region in cathepsin S and risk of asthma in Chinese Han population), however, when I type the rs numbers of the SNP in Ensembl, I got that the SNPs are in different region;

rs7534124; intergenic variant rs1136774; 5 prime UTR variant

How could this be?

[Pierre Lindenbaum]

I type the rs numbers of the SNP in Ensembl,

what is the URL of such observation ? I see only 'intergenic" https://apr2019.archive.ensembl.org/Homo_sapiens/Variation/Context?db=core;r=1:150766097-150767097;v=rs7534124;vdb=variation;vf=502268396

[fatma.mokhtar]

The URL is; https://www.europeanreview.org/article/10833

Answer 1

[ATpoint]

If you check the position in the IGV (panel GENE is the RefSeq annotation, GENCODE is from the gencode project, the variants are the red bars) you see that the one variant is upstream of the first exon of CTSS so outside the gene and by this intergenic. The second one overlaps the first exon which typically is the 5'UTR. Maybe this variant refers to an alternative promoter region that controls this shorter CTSS isoform (but this is thinking aloud). Check the paper on how they defined the promoter region. All I can say is that the annotation intergenic and 5-UTR seems to be correct.