Geography of Genetic Variants Browser

Welcome to the Geography of Genetic Variants (GGV) browser!

To begin, pick a dataset on the dropdown menu. One can search variants within a dataset by its rsID or position (Use the format chromosome#:position, as in, 15:24608502 or chr15:24608502) and clicking the search button or the enter key. Click the "random" button to show a random marker from the chosen dataset.

The embedded IGV browser at the bottom of the page can also also be used to pick a variant for display.

To display the population name, minor allele frequency, minor allele count, and sample size, hover with the mouse over a data point. Click on the plot title to open up the UCSC genome browser at that variant.

Be sure to note we use a notion of a "frequency scale" to display rare variants and a "transparency scale" to indicate uncertain allele frequencies. These are explained in the legend.

If you use the maps in other works, include the source link: http://www.popgen.uchicago.edu/ggv and/or make a formal reference to:
Marcus & Novembre (2016) Visualizing the Geography of Genetic Variants. Bioinformatics.

Keep in mind that this is still an evolving project and many ideas/resources are in progress.

Questions/feedback/ideas/critiques are welcomed and appreciated!
Contact: josephhmarcus at gmail dot com or jnovembre at uchicago dot edu.

To use the embedded IGV Browser, input the number of the chromosome you would like to look at in the search box and hit enter. You can zoom in/out on the chromosome by clicking on the +/- buttons on the right side of the browser. You can zoom in on a specific section of the chromosome by clicking and dragging along the axis.

To move about the chromosome, you can use the arrow keys to move left or right. You can also click and drag on the genes and variants sections if you would like to make smaller movements. To jump to another section of the chromosome, you can click on areas you would like to look at on the upper chromosome display, and the red window will move there.

If you click on a variant (vertical grey bar) in the variants section, then that variant will be displayed on the map above. Also, if you search for a variant in the upper search box by the map, the browser will switch to the variant's chromosome and zoom into that variant's location along the chromosome.

copy paste a single column of snps . Remeber to select the appropriate dataset! submit

Either the SNP you searched is not in the chosen dataset or the search term is formatted incorrectly.

When using the query box, acceptable searches by chromosome/pos or rsID look like...

chr1:742429

1:742429

rs3094315

When using a url-based query, acceptable searches look like:

Query default data (1000 Genomes phase 3) by chromosome and position:
'http://popgen.uchicago.edu/ggv/?chr=10&pos=114900524'

Query default data by rsid:
'http://popgen.uchicago.edu/ggv/?data=1000genomes"&rsid=rs1799983'

Query default data for a random SNP
'http://popgen.uchicago.edu/ggv/?data="1000genomes"&random_snp=True'

Query an alternate dataset:
'http://popgen.uchicago.edu/ggv/?data="1000genomes_superpops"&chr=12&pos=11957847'