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index-queries.html
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<!DOCTYPE html>
<html lang="en">
<head>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-119794696-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-119794696-1');
</script>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="">
<meta name="author" content="">
<link rel="shortcut icon" href="//igv.org/web/img/favicon.ico">
<title>ImmuneRegulation</title>
<!-- Bootstrap CSS - NOT REQUIRED FOR IGV -->
<link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<!-- jQuery UI CSS -->
<link rel="stylesheet" type="text/css" href="//ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/themes/smoothness/jquery-ui.css"/>
<!-- Font Awesome CSS -->
<link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css">
<link rel="shortcut icon" href="//igv.org/web/img/favicon.ico">
<!-- IGV CSS -->
<link rel="stylesheet" type="text/css" href="https://igv.org/web/beta/igv-beta.css">
<!--link rel="stylesheet" type="text/css" href="https://igv.org/web/jb/snapshot/css/igv.css"-->
<!--link rel="stylesheet" type="text/css" href="https://igv.org/web/jb/release/current/igv-beta.css"-->
<!--link rel="stylesheet" type="text/css" href="http://igv.org/web/release/2.0.0-beta1/dist/igv-all.css"-->
<!--link rel="stylesheet" type="text/css" src="./css/beta/igv-beta.css"-->
<!-- IGV GTEx CSS -->
<!--link rel="stylesheet" href="http://igv.org/web/release/1.0.1/igv-1.0.1.css?v=cl80"-->
<!-- IGV Release CSS -->
<!--link rel="stylesheet" type="text/css" href="https://igv.org/web/release/1.0.7/igv-1.0.7.css"-->
<!-- DataTables CSS -->
<link rel="stylesheet" type="text/css" href="//cdn.datatables.net/1.10.13/css/jquery.dataTables.css">
<!--link rel="stylesheet" type="text/css" src="./css/jquery.dataTables.min.css"-->
<link rel="stylesheet" type="text/css" src="./css/typeahead.css">
<!-- jQuery JS -->
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/2.0.3/jquery.min.js"></script>
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js"></script>
<!-- Tooltips -->
<script src="./js/popper.min.js"></script>
<!-- Bootstrap JS - NOT REQUIRED FOR IGV -->
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
<!--script src="./js/bootstrap.js"></script-->
<!-- IGV TEST JS-->
<!-- https://igv.org/web/test/multilocus/igv-multilocus.js -->
<!-- http://igv.org/web/release/1.0.1/igv-1.0.1.min.js -->
<!-- https://igv.org/web/beta/igv-beta.js-->
<!-- IGV JS - DEV -->
<!--script src="./js/igv-selim.js"></script-->
<!-- IGV JS - Deneme DEV -->
<script src="./js/igv-immReg.js"></script>
<!--script src="http://igv.org/web/release/2.0.0-beta1/dist/igv.min.js"></script-->
<!--script src="https://igv.org/web/beta/igv.js"></script-->
<script src="./js/savePng.js"></script>
<script src="https://rawgit.com/exupero/saveSvgAsPng/gh-pages/saveSvgAsPng.js"></script>
<script src="https://rawgit.com/MrRio/jsPDF/master/dist/jspdf.debug.js"></script>
<script src="./js/savePdf.js"></script>
<!-- IGV GTEx JS -->
<!--script src="http://igv.org/web/release/1.0.1/igv-1.0.1.min.js" type="text/javascript"></script-->
<!-- IGV Release JS -->
<!--script type="text/javascript" src="https://igv.org/web/release/1.0.7/igv-1.0.7.js"></script-->
<!-- IGV PROD JS -->
<!--script type="text/javascript" src="https://igv.org/web/beta/igv-beta.js"></script-->
<!-- D3 JS -->
<script src='https://d3js.org/d3.v3.min.js'></script>
<!-- Bootstrap Multi-Select -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-multiselect/0.9.13/js/bootstrap-multiselect.min.js" integrity="sha256-1fK87Pt9T7XXn/Vj3CWSfJlZkL5f73092A8YL7p7avc=" crossorigin="anonymous"></script>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-multiselect/0.9.13/css/bootstrap-multiselect.css" integrity="sha256-O1jJhOIWWDc3wq75g7aXDl7aEQT2XPkieX/Mz/u4hQ0=" crossorigin="anonymous"/>
<link rel="stylesheet" href="//code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css">
<!-- DataTables JS -->
<script type="text/javascript" charset="utf8" src="//cdn.datatables.net/1.10.13/js/jquery.dataTables.js"></script>
<!--script type="text/javascript" charset="utf8" src="./js/jquery.dataTables.min.js"></script-->
<script src="https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js"></script>
<script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script>
<script src="./js/type.js"></script>
<script src="./js/genenames.js"></script>
<script src="./js/uploadFile.js"></script>
<script src="./js/uploadFile2.js"></script>
<script src="./js/underscore-min.js"></script>
<!--script type="text/javascript" src="./js/gwas/t2dVariantSource.js"></script>
<script type="text/javascript" src="./js/gwas/gwasTrack.js"></script-->
<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
<script type="text/javascript">
$( function() {
$(document).tooltip({
position: {
my: "center bottom-20",
at: "center top",
using: function( position, feedback ) {
$( this ).css( position );
$( "<div>" )
.addClass( "arrow" )
.addClass( feedback.vertical )
.addClass( feedback.horizontal )
.appendTo( this );
}
}
});
} );
$(document).ready(function() {
$('#datasetT').multiselect({
enableClickableOptGroups: true,
enableCollapsibleOptGroups: true,
buttonWidth: '350px',
nonSelectedText: 'Choose dataset(s)'
});
$('.multiselect-container').find(".caret").click();
$("body").tooltip({ selector: '[data-toggle=tooltip]' });
$("#studyEntryRow").hide();
$("#operationEntryRow").hide();
//User Studies...
$("#userListMain").hide();
$("#userListCis").hide();
$("#userListTrans").hide();
$("#allStudies li:contains(User)").hide();
//$("#userListTrans0").hide();
//$("#userListInput").hide();
//Multiple Select Deneme
/* $('#geneDataSelect').multiselect({
enableFiltering: true,
includeSelectAllOption: true,
maxHeight: 200
}); */
//Update studyCountText
var allcheckboxes = document.querySelectorAll('input.studyopt');
for(var i = 0; i < allcheckboxes.length; i++) {
allcheckboxes[i].onclick = function() {
var allcheckedcount = document.querySelectorAll('input.studyopt:checked').length;
document.getElementById('studyCountText').innerText = allcheckedcount + " studies selected";
if(allcheckedcount > 0)
document.getElementById('deselectDiv').style.visibility = "visible";
else
document.getElementById('deselectDiv').style.visibility = "hidden";
}
}
//Emory Checkboxes
var emorycheckboxes = document.querySelectorAll('input.EmoryOption');
var emorycheckall = document.getElementById('EmoryCheckAll');
for(var i = 0; i < emorycheckboxes.length; i++) {
emorycheckboxes[i].onclick = function() {
var emoryCheckCount = document.querySelectorAll('input.EmoryOption:checked').length;
emorycheckall.checked = emoryCheckCount > 0;
emorycheckall.indeterminate = emoryCheckCount > 0 && emoryCheckCount < emorycheckboxes.length;
var allcheckedcount = document.querySelectorAll('input.studyopt:checked').length;
document.getElementById('studyCountText').innerText = allcheckedcount + " studies selected";
if(allcheckedcount > 0)
document.getElementById('deselectDiv').style.visibility = "visible";
else
document.getElementById('deselectDiv').style.visibility = "hidden";
}
}
emorycheckall.onclick = function() {
for(var i = 0; i < emorycheckboxes.length; i++) {
emorycheckboxes[i].checked = this.checked;
}
var allcheckedcount = document.querySelectorAll('input.studyopt:checked').length;
document.getElementById('studyCountText').innerText = allcheckedcount + " studies selected";
if(allcheckedcount > 0)
document.getElementById('deselectDiv').style.visibility = "visible";
else
document.getElementById('deselectDiv').style.visibility = "hidden";
}
//Mayo Checkboxes
var mayocheckboxes = document.querySelectorAll('input.MayoOption');
var mayocheckall = document.getElementById('MayoCheckAll');
for(var i = 0; i < mayocheckboxes.length; i++) {
mayocheckboxes[i].onclick = function() {
var mayoCheckCount = document.querySelectorAll('input.MayoOption:checked').length;
mayocheckall.checked = mayoCheckCount > 0;
mayocheckall.indeterminate = mayoCheckCount > 0 && mayoCheckCount < mayocheckboxes.length;
var allcheckedcount = document.querySelectorAll('input.studyopt:checked').length;
document.getElementById('studyCountText').innerText = allcheckedcount + " studies selected";
if(allcheckedcount > 0)
document.getElementById('deselectDiv').style.visibility = "visible";
else
document.getElementById('deselectDiv').style.visibility = "hidden";
}
}
mayocheckall.onclick = function() {
for(var i = 0; i < mayocheckboxes.length; i++) {
mayocheckboxes[i].checked = this.checked;
}
var allcheckedcount = document.querySelectorAll('input.studyopt:checked').length;
document.getElementById('studyCountText').innerText = allcheckedcount + " studies selected";
if(allcheckedcount > 0)
document.getElementById('deselectDiv').style.visibility = "visible";
else
document.getElementById('deselectDiv').style.visibility = "hidden";
}
//Yale Checkboxes
var yalecheckboxes = document.querySelectorAll('input.YaleOption');
var yalecheckall = document.getElementById('YaleCheckAll');
for(var i = 0; i < yalecheckboxes.length; i++) {
yalecheckboxes[i].onclick = function() {
var yaleCheckCount = document.querySelectorAll('input.YaleOption:checked').length;
yalecheckall.checked = yaleCheckCount > 0;
yalecheckall.indeterminate = yaleCheckCount > 0 && yaleCheckCount < yalecheckboxes.length;
var allcheckedcount = document.querySelectorAll('input.studyopt:checked').length;
document.getElementById('studyCountText').innerText = allcheckedcount + " studies selected";
if(allcheckedcount > 0)
document.getElementById('deselectDiv').style.visibility = "visible";
else
document.getElementById('deselectDiv').style.visibility = "hidden";
}
}
yalecheckall.onclick = function() {
for(var i = 0; i < yalecheckboxes.length; i++) {
yalecheckboxes[i].checked = this.checked;
}
var allcheckedcount = document.querySelectorAll('input.studyopt:checked').length;
document.getElementById('studyCountText').innerText = allcheckedcount + " studies selected";
if(allcheckedcount > 0)
document.getElementById('deselectDiv').style.visibility = "visible";
else
document.getElementById('deselectDiv').style.visibility = "hidden";
}
});
</script>
<style type="text/css">
.ui-tooltip, .arrow:after {
background: white;
border: 2px solid white;
}
.ui-tooltip {
padding: 10px 20px;
color: black;
border-radius: 10px;
font: bold 14px "Helvetica Neue", Sans-Serif;
box-shadow: 0 0 7px black;
opacity: 0.9;
}
.arrow {
width: 70px;
height: 16px;
overflow: hidden;
position: absolute;
left: 50%;
margin-left: -35px;
bottom: -16px;
}
.arrow.top {
top: -16px;
bottom: auto;
}
.arrow.left {
left: 20%;
}
.arrow:after {
content: "";
position: absolute;
left: 20px;
top: -20px;
width: 25px;
height: 25px;
box-shadow: 6px 5px 9px -9px black;
-webkit-transform: rotate(45deg);
-ms-transform: rotate(45deg);
transform: rotate(45deg);
}
.arrow.top:after {
bottom: -20px;
top: auto;
}
#custom-search-input {
margin:0;
margin-top: 10px;
padding: 0;
}
#custom-search-input .search-query {
padding-right: 3px;
padding-right: 4px \9;
padding-left: 3px;
padding-left: 4px \9;
/* IE7-8 doesn't have border-radius, so don't indent the padding */
margin-bottom: 0;
-webkit-border-radius: 3px;
-moz-border-radius: 3px;
border-radius: 3px;
}
#custom-search-input button {
border: 0;
background: none;
/** belows styles are working good */
padding: 2px 5px;
margin-top: 2px;
position: relative;
left: -28px;
/* IE7-8 doesn't have border-radius, so don't indent the padding */
margin-bottom: 0;
-webkit-border-radius: 3px;
-moz-border-radius: 3px;
border-radius: 3px;
color:#D9230F;
}
.search-query:focus + button {
z-index: 3;
}
.graph-svg-component {
background-color: AliceBlue;
}
.filter {
display: inline-block;
}
#geneSearch, #uploadStudy, #saveModal, #vizListButton {
background: #1974B8;
}
#geneSearch:hover, #uploadStudy:hover, #saveModal:hover, #vizListButton:hover {
background: #035b9c;
}
#geneSearch:active, #vizListButton:active {
background: #1974B8;
}
.btn, .btn-primary {
background: white;
padding: 14px 24px;
font-weight: 400;
letter-spacing: 1px;
border-radius: 0;
border: 1 solid;
border-color: #bbb;
}
.btn-group, .btn-group-vertical {
margin-left: 10px;
}
.btn:focus, .btn:active:focus, .btn.active:focus {
outline: 0 none;
border: 2 solid;
border-color: #bbb;
}
.btn-primary.active, .btn-primary:focus, .btn-primary:active, .open > .dropdown-toggle.btn-primary {
background: lightgray;
color: #000;
box-shadow: none;
border: 1 solid;
border-color: #bbb;
}
.btn-primary:hover {
background: #bbb;
border: 1 solid;
border-color: #bbb;
}
.btn-primary:active, .btn-primary.raised.active {
background: lightgray;
box-shadow: none;
margin-bottom: -3px;
margin-top: 3px;
border: 1 solid;
border-color: #bbb;
}
.btn-primary.disabled, .btn-primary.disabled:focus, .btn-primary.disabled:active {
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color: white;
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<a id="exQuery1" href="#" onclick="exampleQuery1();">Example 1 - Cis-eQTLs for JAK2 gene in monocyte exposure studies</a>
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<a id="exQuery3" href="#" onclick="exampleQuery3();">Example 3 - Transcription Factor studies with hits for IL17A gene </a>
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<p style="font-size:medium; text-align:center;"><strong> immuneRegulation </strong> provides visualization, exploration, and download of large-number of regulatory data through a single, and intuitive interface.
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<div class="row" id="geneEntryRow" style="border:1px solid #888888; margin-top: 10px;margin-left:-5px;margin-right:-5px; padding-top:10px;">
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<p style=""><strong> Enter Gene(s): </strong></p>
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<div class="col-md-6" style="font-size:medium;">
<textarea id="geneVal" class="typeahead" placeholder="Enter HUGO Gene symbols" cols="57" rows="4" style="padding-top:0px; margin-bottom:5px; overflow:inherit;overflow-x: hidden;"></textarea>
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<p style=""> Please enter a single gene in the gene-box for 'cis-eQTL' queries. </p>
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<span style="margin-right:5px;" class="glyphicon glyphicon-list"> </span> <strong> Study List: </strong>
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<p id="studyCountText"> 0 studies selected </p>
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<a href="#" onclick = "deselectStudies()"> Deselect all </a>
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<p> <strong>Study Type: </strong> </p>
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<div class="col-md-2" style = "font-size:medium; color:#337ab7; text-align:left; padding-top:20px; opacity:0.5;">
<p id="queryType"> Not Selected </p>
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</div>
<div class="row" style="padding:0px; overflow: hidden; height:91%; margin:0px;">
<div class="col-md-3" style="padding:0px; overflow: scroll; height:inherit; background:white;">
<ul class="list-group" style="margin-bottom: 0px; font-size:initial;">
<li class="list-group-item" id="userListMain" style="color:black; background:#a1cce4;">
<span class="badge" id="userListCount">0</span>
<a href="#" onClick = filterUser()> ⇣ User Studies </a>
</li>
<li class="list-group-item" id="userListCis" style="color:black; padding-left:35px;background:#a1cce4;">
<span class="badge" id="userListCisCount">0</span>
<a href="#" onClick = filterCisUser()> ↳ cis-eQTL</a>
</li>
<li class="list-group-item" id="userListTrans" style="color:black; padding-left:35px;background:#a1cce4;">
<span class="badge" id="userListTransCount">0</span>
<a href="#" onClick = filterTransUser()> ↳ trans-eQTL</a>
</li>
<li class="list-group-item" id="listHIPC" style="color:black; background:#a1cce4;">
<span class="badge">22</span>
<a href="#" onClick = filterHIPC()>
<!--span style="margin-right:5px;" class="glyphicon glyphicon-option-vertical"> </span--> ⇣ HIPC Studies </a>
</li>
<li class="list-group-item" id="listCisHIPC" style="color:black; padding-left:35px; background:#a1cce4;">
<span class="badge">11</span>
<a href="#" onClick = filterCisHIPC()>
<!--span style="margin-right:5px;" class="glyphicon glyphicon-option-vertical"> </span>
<span style="margin-right:5px;" class="glyphicon glyphicon-option-vertical"> </span--> ↳ cis-eQTL</a>
</li>
<li class="list-group-item" id="listTransHIPC" style="color:black; padding-left:35px; background:#a1cce4;">
<span class="badge">11</span>
<a href="#" onClick = filterTransHIPC()>
<!--span style="margin-right:5px;" class="glyphicon glyphicon-option-vertical"> </span>
<span style="margin-right:5px;" class="glyphicon glyphicon-option-vertical"> </span--> ↳ trans-eQTL</a>
</li>
<li class="list-group-item" id="listNonHIPC" style="color:black;background:#a1cce4;">
<span class="badge">37</span>
<a href="#" onClick = filterNonHIPC()>
<!--span style="margin-right:5px;" class="glyphicon glyphicon-option-vertical"> </span--> ⇣ Non-HIPC Studies </a>
</li>
<li class="list-group-item" id="listCisNonHIPC" style="color:black; padding-left:35px;background:#a1cce4;">
<span class="badge">23</span>
<a href="#" onClick = filterCisNonHIPC()>
<!--span style="margin-right:5px;" class="glyphicon glyphicon-menu-right"> </span>
<span style="margin-right:5px;" class="glyphicon glyphicon-option-horizontal"> </span--> ↳ cis-eQTL</a>
</li>
<li class="list-group-item" id="listTransNonHIPC" style="color:black; padding-left:35px;background:#a1cce4;">
<span class="badge">14</span>
<a href="#" onClick = filterTransNonHIPC()>
<!--span style="margin-right:5px;" class="glyphicon glyphicon-menu-right"> </span>
<span style="margin-right:5px;" class="glyphicon glyphicon-option-horizontal"> </span--> ↳ trans-eQTL</a>
</li>
<li class="list-group-item" id="mainTF" style="color:black;background:#a1cce4;">
<span class="badge">1945</span>
<a href="#" onClick = filterTF()>
<!--span style="margin-right:5px;" class="glyphicon glyphicon-option-vertical"> </span--> ⇣ Transcription Factors </a>
</li>
</ul>
</div>
<div class="col-md-9" style="padding-left:0px; overflow: scroll; height:inherit; padding-right:0px; background:white;">
<ul class="list-group" id="allStudies" style="margin-bottom: 0px; font-size:initial; ">
<li class="list-group-item user" id="UserListTitle" style="color:black; padding-top:15px;padding-left:10px;">
<strong>User Studies</strong>
</li>
<li class="list-group-item user ucis" id="UserListCis0" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study101" value="on">
<span value="101" id="span1000">User</span>
</li>
<li class="list-group-item user ucis" id="UserListCis1" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study102" value="on">
<span value="102" id="span1001">User</span>
</li>
<li class="list-group-item user ucis" id="UserListCis2" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study103" value="on">
<span value="103" id="span1002">User</span>
</li>
<li class="list-group-item user utrans" id="UserListTrans0" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study111" value="on">
<span value="111" id="span1100">User</span>
</li>
<li class="list-group-item user utrans" id="UserListTrans1" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study112" value="on">
<span value="112" id="span1101">User</span>
</li>
<li class="list-group-item user utrans" id="UserListTrans2" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study113" value="on">
<span value="113" id="span1102">User</span>
</li>
<li class="list-group-item user" id="UserListCis" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<!-- <input type="checkbox" class="studyopt Option" id="study102" value="on">
<span value="102" id="span102">User</span> -->
</li>
<li class="list-group-item non-hipc" style="color:black; padding-top:15px;padding-left:10px;">
<strong>Non-HIPC Studies</strong>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-left:30px; border-bottom:0px;">
<strong>Whole Blood</strong>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="framingham" value="on">
<span value="11">Whole Blood - European American (Framingham Heart Study, NHLBI)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 5257 samples </span>
<span class="glyphicon glyphicon-info-sign" aria-hidden="true" data-toggle="tooltip" title="Framingham Heart Study, under the direction of the National Heart, Lung and Blood Institute (NHLBI), formerly known as the National Heart Institute, has been committed to identifying the common factors or characteristics that contribute to cardiovascular disease (CVD). Study began in 1948 by recruiting an Original Cohort of 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, who had not yet developed overt symptoms of cardiovascular disease or suffered a heart attack or stroke."></span>
<a href="https://www.framinghamheartstudy.org/" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc cis" style="color:black;padding-top:5px;padding-bottom:5px;border-bottom:0px;padding-left:30px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="gtex" value="on">
<span value="12">Whole Blood - Mixed ethnicity - GTEx Consortium (Science, 2015)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 338 samples </span>
<span class="glyphicon glyphicon-info-sign" title="The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes." aria-hidden="true"></span>
<a href="https://gtexportal.org/home/" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px; border-top:0px;border-bottom:0px;">
<input type="checkbox" class="studyopt Option" id="westra" value="on">
<span value="13">Whole Blood - Meta-analysis - European (Nature Genetics, 2013)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 5311 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Authors performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. They identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance." aria-hidden="true"></span>
<a href="http://genenetwork.nl/bloodeqtlbrowser/" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc cis" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px; border-top:0px;border-bottom:0px;">
<input type="checkbox" class="studyopt Option" id="study14" value="on">
<span value="14">Whole Blood - European (Nature Genetics, 2017)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 2166 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Authors generated peripheral blood RNA–seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers." aria-hidden="true"></span>
<a href="https://www.nature.com/articles/ng.3737" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px; border-top:0px;border-bottom:0px;">
<input type="checkbox" class="studyopt Option" id="study15" value="on">
<span value="15">Whole Blood - East Asian (PLoS Genetics, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 1799 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Authors use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine if observed trans-eQTL associations are mediated by expression of transcripts in cis with the SNPs showing trans-association, using Sobel tests of mediation." aria-hidden="true"></span>
<a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004818" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px; border-top:0px;border-bottom:0px;">
<input type="checkbox" class="studyopt Option" id="study16" value="on">
<span value="16">Whole Blood - East Asian (PLoS One, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 298 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, authors mapped expression quantitative trait loci (eQTLs)." aria-hidden="true"></span>
<a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100924" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-left:30px; border-bottom:0px;">
<strong>Monocytes</strong>
</li>
<li class="list-group-item non-hipc cis" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study21" value="on">
<span value="21">Monocytes - African American (Science, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 162 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. Authors note an over-representation of T cell–specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer’s and Parkinson’s disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants." aria-hidden="true"></span>
<a href="http://science.sciencemag.org/content/344/6183/519" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc cis" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-top:0px;border-bottom:0px;">
<input type="checkbox" class="studyopt Option" id="study22" value="on">
<span value="22">Monocytes - East Asian (Science, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 155 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. Authors note an over-representation of T cell–specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer’s and Parkinson’s disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants." aria-hidden="true"></span>
<a href="http://science.sciencemag.org/content/344/6183/519" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc cis" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px; border-top:0px;border-bottom:0px;">
<input type="checkbox" class="studyopt Option" id="study23" value="on">
<span value="23">Monocytes - European American (Science, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 377 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. Authors note an over-representation of T cell–specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer’s and Parkinson’s disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants." aria-hidden="true"></span>
<a href="http://science.sciencemag.org/content/344/6183/519" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc trans" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study24" value="on">
<span value="24">Monocytes - Meta-analysis (Science, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 696 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. Authors note an over-representation of T cell–specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer’s and Parkinson’s disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants." aria-hidden="true"></span>
<a href="http://science.sciencemag.org/content/344/6183/519" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study25" value="on">
<span value="25">Monocytes - European (Nature Genetics, 2012)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 288 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Using paired purified primary monocytes and B cells, authors identify new predominantly cell type–specific cis and trans expression quantitative trait loci (eQTLs), including multi-locus trans associations to LYZ and KLF4 in monocytes and B cells, respectively. " aria-hidden="true"></span>
<a href="http://www.nature.com/ng/journal/v44/n5/full/ng.2205.html" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px; border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study26" value="on">
<span value="26">Monocytes - European American (Science, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 432 samples </span>
<span class="glyphicon glyphicon-info-sign" title="To systematically investigate the impact of immune stimulation upon regulatory variant activity, we exposed primary monocytes from 432 healthy Europeans to interferon-γ (IFN-γ) or differing durations of lipopolysaccharide and mapped expression quantitative trait loci (eQTLs). More than half of cis-eQTLs identified, involving hundreds of genes and associated pathways, are detected specifically in stimulated monocytes." aria-hidden="true"></span>
<a href="http://science.sciencemag.org/content/343/6175/1246949" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc" style="color:black;padding-top:5px;padding-left:30px; border-bottom:0px;">
<strong>CD4+ T-cells</strong>
</li>
<li class="list-group-item non-hipc cis" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study31" value="on">
<span value="31">CD4+ T-cells - African American (Science, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 162 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. Authors note an over-representation of T cell–specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer’s and Parkinson’s disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants." aria-hidden="true"></span>
<a href="http://science.sciencemag.org/content/344/6183/519" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc cis" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study32" value="on">
<span value="32">CD4+ T-cells - East Asian (Science, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 155 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. Authors note an over-representation of T cell–specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer’s and Parkinson’s disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants." aria-hidden="true"></span>
<a href="http://science.sciencemag.org/content/344/6183/519" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc cis" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px; border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study33" value="on">
<span value="33">CD4+ T-cells - European American (Science, 2014)</span>
<span style = "float:right;"> <span style = "color:gray; font-size:smaller;"> 377 samples </span>
<span class="glyphicon glyphicon-info-sign" title="Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. Authors note an over-representation of T cell–specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer’s and Parkinson’s disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants." aria-hidden="true"></span>
<a href="http://science.sciencemag.org/content/344/6183/519" target="_blank"> <span class="glyphicon glyphicon-book" aria-hidden="true"></span></span> </a>
</li>
<li class="list-group-item non-hipc trans" style="color:black;padding-top:5px;padding-bottom:5px;padding-left:30px;border-bottom:0px;border-top:0px;">
<input type="checkbox" class="studyopt Option" id="study34" value="on">