I tried to use NCBI to check for the location of a SNP in the 3UTR OF a gene, by using SNP:GENE VIEW , but, I didn`t find my SNP of interest in the (in gene region) option?
1. Search your gene in NCBI
2. Save several (the more the better) sequence of the gene (I use 15-30)
3. Align sequences and find mismatches...
Note: did you use the latest dbSNP version? I assume that you have a known SNP (you known the rs of that SNP) and you are willing to visualize it within the 3'-UTR of a known gene. I would suggest you use the UCSC genome browser. Open the browser, enter the name of your gene of interest in the search region and browse. Than choose to display the full SNP track. You can than find you SNP and visualize its precise position within the gene. If you zoom-in you can visualize the SNP and the flanking sequence. Here is an example for the FGFR2 gene where I displayed the full SNP track for dbSNP142 (http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr10%3A123237844-123353481&hgsid=436894733_THojrfZFJr5Rt8IBemaPtjA5LQav).
Try finding it on dbsnp or ucsc browser. The position might vary depending upon the assembly. Use the latest assembly, preferably.
For variations in human coding regions, ExAC has data from 63,000 humans over several major population groups, and is always worth checking.
http://exac.broadinstitute.org
Thanks all for your helpful answers, I will try the methods that you mentioned.
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