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<!doctype html>
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<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
<title>GGV</title>
<link rel="icon" href="/css/map.ico">
<meta name="description" content="">
<meta name="author" content="">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<link rel="stylesheet" href="css/style.css">
</head>
<body>
<div class="container" id='all'>
<div id="main" role="main">
<a href="https://twitter.com/share" class="twitter-share-button">Tweet</a>
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs');</script>
<h1>Geography of Genetic Variants Browser<p id='sub'>Beta v0.1</p></h1>
<a data-toggle="modal" data-target="#myModal" id='about'><p id='about'>About / Help</p></a>
<div class="modal fade" id="myModal" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h4 class="modal-title" id="myModalLabel">About</h4>
</div>
<div class="modal-body">
Welcome to the Geography of Genetic Variants (GGV) browser! <br><br> 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. Otherwise click
the "random" button to show a random marker from the chosen dataset. One can also hover over a pie
chart to display the population name, minor allele frequency, minor allele count, and sample size. Click on the position title to open up the UCSC genome browser at that variant.
<br><br>Be sure to note we use a notion of a "frequency scale" to display rare variants. This is explained in the lower left with a legend.
<br><br>
If you use the maps in other works, include the source link: <a href=http://www.popgen.uchicago.edu/ggv/>http://www.popgen.uchicago.edu/ggv</a>
and/or make a formal reference to:<br> <i>JH Marcus and J Novembre. Geography of Genetic Variants Browser v0.1. http://www.popgen.uchicago/ggv/</i>.
<br><br>Keep in mind that this
is still a rough draft and many ideas/resources are in progress.
<br><br> Questions/feedback/ideas/critiques are welcomed and appreciated! <br>Contact: josephhmarcus at gmail dot com
<br><br>
</div>
</div>
</div>
</div>
<div class="modal fade" id="upload" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h4 class="modal-title" id="myModalLabel"><i class="fa fa-list-ol"></i></h4>
</div>
<div class="modal-body">
<form id='snpArea'>
copy paste a single column of snps <i class="fa fa-long-arrow-down"></i>. Remeber to select the appropriate dataset!
<textarea id='snp_col' class="form-control" rows="3" type="text"></textarea>
<button id='submitArea' type="button" class="btn btn-default">submit</button>
</form>
</div>
</div>
</div>
</div>
<div class='row' id='settings'>
<div id="dropDown" class='col-sm-4'>
<div id='datasets'>
</div>
</div>
<div class='col-sm-4'>
<div id='variant_settings'>
<div>
<form id='buttons' class='btn-group' onSubmit="return false;">
<input id='search' type="text" class="form-control" placeholder='rsID/chr#:pos'>
<button id='submit' type="button" class="btn btn-default"><i class="fa fa-search"></i></button>
<button id='random' type='button' class="btn btn-default">random</button>
<button id='upload' type='button' class="btn btn-default" data-toggle="modal" data-target="#upload"><i class="fa fa-list-ol"></i></button>
</form>
</div>
</div>
</div>
<div id="layouts" class='col-sm-4'>
<div class="btn-group">
<a id="true" class="btn btn-default">True Position</a>
<a id="charged" class="btn btn-default">Avoid Overlap</a>
</div>
</div>
<div class='col-sm-12' id='slider-holder'>
<div id="slider"></div>
</div>
</div>
<div class="modal fade" id="alert" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h4 class="modal-title" id="myModalLabel"><i class="fa fa-exclamation-triangle"></i></h4>
</div>
<div class="modal-body">
Either the SNP you searched is not in the chosen dataset or the search term is formatted incorrectly. Acceptable searchs by chromosome/pos or rsID look like...<br><br>
chr1:742429
<br>
1:742429
<br>
rs3094315
<br>
</div>
</div>
</div>
</div>
<div id="vis">
<div id='variant'><h2></h2></div>
</div>
<div class="row" id='legend'>
<div id='freqLegend' class="col-sm-4">
<h3></h3>
<p></p>
</div>
<div id='transLegend' class="col-sm-4">
<h3></h3>
<p></p>
</div>
<div id='testLegend' class="col-sm-4">
<h3></h3>
<p></p>
</div>
</div>
</div>
</div>
<footer id='footer'>
<div id='text'>
<p><a href='http://jnpopgen.org/' target='_blank'>Novembre Lab</a><br>Developed by Joe Marcus and John Novembre<br>Department of Human Genetics, University of Chicago</p>
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