I have a specific DNA sequence which I could determine its location in a specific gene in the human genome. I wonder how can I know if it is located in a SNP region or no? And if it is in intron or exon?
If you've got a sequence, put it into [Ensembl BLAST](http://www.ensembl.org/Multi/Tools/Blast?db=core). The results will tell you if it falls in a gene, and gives you a link to click on the location, where you'll see the sequence highlighted in red. There will also be tracks showing the structure of the genes and variants in the region.
or you blast the sequence in the UCSC website and you'll have directly the location (https://genome.ucsc.edu/cgi-bin/hgBlat).
fred
Hello dear colleague,
I recommend using "UCSC" genome browser. To use it, go to google and type UCSC. then, go to "tools" and "blat" icons on top of its hompage and paste your sequence.
Finally click on browser in the result page to go onto a graphic page. All SNPs can be displayed in this page. get other information about working with UCSC from tutorial of youtube (for example).
Good luck.
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