How do I find all the SNPs in a gene using the UCSC Genome Browser?
This tutorial will demonstrate how to find all the single nucleotide polymorphisms in agene using the UCSC Genome Browser.
To start we will go to the Genome Browser at genome.ucsc.edu and in the upper lefthand corner are two links that take us to the main page of the Browser where we canchoose which organism to use. We will use the human default assembly hg19. The“click here to reset” button takes us to the default location and the [submit] button
then will take us to the Browser graphical viewer.
[0:43] The default data are shown here, a number of data tracks. We will simplify theview by hiding all the data tracks and then we will turn the UCSC Genes track on to“pack” and hit the [refresh] button. The default gene here is the SOD1 gene. We will
go to another gene, the SRC gene and choose that from the list and the [go] button willtake us there. So the reason to show you this gene is to demonstrate that occasionallythe canonical gene for a particular gene is not the largest transcript and if you’reinterested in getting the SNPs for all parts of the gene, you will want to widen thewindow just a little bit. We will nudge the window by opening it up using the little left
arrow on the side here.
[1:35] Now the tracks for the single nucleotide polymorphisms are at the bottom of thescreen and we will turn on three of those tracks: the Common SNPs from dbSnp
version 138, the All SNPs track from the same version, and the Flagged SNPs track
which are the clinically relevant or potentially clinically relevant polymorphisms. The
refresh button then turns on all of those tracks to “pack”, and we see that we get a verylarge number of SNPs with their rs numbers in the screen. The red ones are amino acidchanges, the blue ones are splice sites or untranslated regions, the black ones are
intronic regions.
Now the right mouse button will let us collapse the track down to a single row where it is“dense” and you can see that they’re well distributed throughout the gene here. The All
SNPs track is considerably denser that the Common SNPs track as you would expect
and then finally the clinically relevant SNPs also include some green ones which arecoding region SNPs that have no change in amino acid. We will collapse them as welldown to “dense.” Now they may or may not be clinically relevant and it is necessary tounderstand the exact nature of this track by reading the track description underneaththe button on the left side. That’s where you will learn that they are clinically relevant if
they have a particular flag from NCBI where they’re designated as having been
contributed by a locus-specific database. This does not mean that they are necessarily
disease-causing.
So now that we have seen the various types of SNP tracks there are, the All SNPs isthe generally overarching track the other two are subsets of the all SNPs track. We will
go to the Table Browser and use one of these tracks to find the SNPs in the gene.

[3:27] We will simply get the SNPs in this particular gene and the genome browser
remembers where we were on the previous screen so that the coordinates are preloaded into this but it is necessary to click the [position] button. To find the SNP tracks
we will select the variation group to match their location in the track controls beneath theGenome Browser graphical display. We will use the Common SNP track in thisdemonstration and we will get a list of SNPs. For “output format:” we choose“selected fields from primary and related tables” to get to a page where we canpick the columns we wish to save. And then the [get output] button takes us to a place
where we can choose which features we wish to download as part of our file. On thispage we can choose the name of the SNP. (We) can also choose the genomic
coordinates if we’re interested. For the moment we’ll just choose the name. We canalso choose a number of different items, such as the “function” and the “allelefrequency” from this list. The [get output] button takes us to the list of SNPs.
[4:36] Now to demonstrate that we have the list we really want let’s just choose just thers numbers from the list, we’ll leave the header behind, and we will copy this list backinto the Table Browser and use it to generate a custom track so we can visualize ourSNPs on the Genome Browser. And then the [Back] button takes us back and we will
use the pull down menu to go to the main page of the Table Browser. Using the [pastelist] button we will go to the page where we can load our SNPs into the Table Browser.
The [submit] button loads the list of SNPs and then the “output format” button lets us
choose “custom track” for our output.
The [get output] button takes us to a place where we can label our track. We will call it“common SNPS in SRC” and we will call the long label “common SNPs in SRC gene region”
and use [get output] to see the custom track. And we will go over to the genome
browser and view them. We can see the rs numbers and the tick marks corresponding
to them. We will collapse them down into “dense.”
Now the Common SNPs track can be moved up into place so that they are side by sidewith the new track we just created and we’ll select this exon over here so that we canzoom into the region and get a closer look. You can see that there’s a match between
our newly formed track and the original Common SNPs track from which it derived.
Now to see how we did restricting the range of our query, let’s zoom out by a factor of
100 and we can see that all of the SNPs in our new track are situated over the SRC
gene.