Overlay example

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var layer = new ol.layer.Tile({
  source: new ol.source.MapQuest({layer: 'sat'})
});

var map = new ol.Map({
  layers: [layer],
  target: 'map',
  view: new ol.View({
    center: [0, 0],
    zoom: 2
  })
});

var pos = ol.proj.fromLonLat([16.3725, 48.208889]);

// Vienna marker
var marker = new ol.Overlay({
  position: pos,
  positioning: 'center-center',
  element: document.getElementById('marker'),
  stopEvent: false
});
map.addOverlay(marker);

// Vienna label
var vienna = new ol.Overlay({
  position: pos,
  element: document.getElementById('vienna')
});
map.addOverlay(vienna);

// Popup showing the position the user clicked
var popup = new ol.Overlay({
  element: document.getElementById('popup')
});
map.addOverlay(popup);

map.on('click', function(evt) {
  var element = popup.getElement();
  var coordinate = evt.coordinate;
  var hdms = ol.coordinate.toStringHDMS(ol.proj.transform(
      coordinate, 'EPSG:3857', 'EPSG:4326'));

$(element).popover('destroy');
  popup.setPosition(coordinate);
  // the keys are quoted to prevent renaming in ADVANCED mode.
  $(element).popover({
    'placement': 'top',
    'animation': false,
    'html': true,
    'content': '<p>The location you clicked was:</p><code>' + hdms + '</code>'
  });
  $(element).popover('show');
});

<!DOCTYPE html>
<html>
<head>
<title>Overlay example</title>
<script src="https://code.jquery.com/jquery-1.11.2.min.js"></script>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js"></script>
<link rel="stylesheet" href="http://openlayers.org/en/v3.9.0/css/ol.css" type="text/css">
<script src="http://openlayers.org/en/v3.9.0/build/ol.js"></script>
<link rel="stylesheet" href="overlay.css">
<style>
#marker {
  width: 20px;
  height: 20px;
  border: 1px solid #088;
  border-radius: 10px;
  background-color: #0FF;
  opacity: 0.5;
}
#vienna {
  text-decoration: none;
  color: white;
  font-size: 11pt;
  font-weight: bold;
  text-shadow: black 0.1em 0.1em 0.2em;
}
.popover-content {
  min-width: 180px;
}

</style>
</head>
<body>
<div class="container-fluid">

<div class="row-fluid">
  <div class="span12">
    <div id="map" class="map"></div>
  </div>
</div>
<div style="display: none;">
  <!-- Clickable label for Vienna -->
  <a class="overlay" id="vienna" target="_blank" href="http://en.wikipedia.org/wiki/Vienna">Vienna</a>
  <div id="marker" title="Marker"></div>
  <!-- Popup -->
  <div id="popup" title="Welcome to ol3"></div>
</div>

</div>
<script>
var layer = new ol.layer.Tile({
  source: new ol.source.MapQuest({layer: 'sat'})
});

var map = new ol.Map({
  layers: [layer],
  target: 'map',
  view: new ol.View({
    center: [0, 0],
    zoom: 2
  })
});

var pos = ol.proj.fromLonLat([16.3725, 48.208889]);

// Vienna marker
var marker = new ol.Overlay({
  position: pos,
  positioning: 'center-center',
  element: document.getElementById('marker'),
  stopEvent: false
});
map.addOverlay(marker);

// Vienna label
var vienna = new ol.Overlay({
  position: pos,
  element: document.getElementById('vienna')
});
map.addOverlay(vienna);

// Popup showing the position the user clicked
var popup = new ol.Overlay({
  element: document.getElementById('popup')
});
map.addOverlay(popup);

map.on('click', function(evt) {
  var element = popup.getElement();
  var coordinate = evt.coordinate;
  var hdms = ol.coordinate.toStringHDMS(ol.proj.transform(
      coordinate, 'EPSG:3857', 'EPSG:4326'));

  $(element).popover('destroy');
  popup.setPosition(coordinate);
  // the keys are quoted to prevent renaming in ADVANCED mode.
  $(element).popover({
    'placement': 'top',
    'animation': false,
    'html': true,
    'content': '<p>The location you clicked was:</p><code>' + hdms + '</code>'
  });
  $(element).popover('show');
});

</script>
</body>
</html>