In biological databases like dbSNP, UCSC Genome Browser, some SNPs are mentioned with more than one function like intron variant, upstream variant 2KB, missense. For example, rs16947. I would like to know, how a SNP can be an intron variant as well as / or upstream variant 2KB.
Tommaso Mazza
This simply happens when your gene has more than one isoforms, one, for example, shorter than the other, either from the 5' or from the 3'. In this case, if your variant falls between the first and second exons of one isoform and the TSS of the 2nd isoform falls around the second exon, you can have that the annotation tools correctly annotate this SNP both as intronic and as upstream.
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