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lovd2_REP1.html
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<!DOCTYPE HTML>
<HEAD>
<TITLE>FinDis</TITLE>
<!--script>
document.write('<div id="loading"><p><b>LOADING</b>...</p></div><style type="text/css">#wrapper{visibility:hidden}#loading{margin:100px auto;width:480px;border:5px solid #777;padding:20px;text-align:left;}</style>');
</script-->
</HEAD>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script>
<script src="js_css/jquery.tools.min.js"></script>
<script language="javascript" src="js_css/jquery.transform.js"></script>
<script type="text/javascript" src="js_css/smooth.pack.js"></script>
<style type="text/css">
body {
padding-top: 60px;
padding-bottom: 40px;
padding-left: 60px;
}
</style>
<link rel="stylesheet" type="text/css" href="js_css/standalone.css">
<link rel="stylesheet" type="text/css" href="js_css/styles.css">
<style>
a:hover {
color:#red;
}
#gene_info {
color: grey;
}
div.wrap {
width:830px;
margin-bottom:40px;
margin-left: auto ;
margin-right: auto ;
background:white;
}
.wrap .pane {
font-size:14px;
display:none;
padding:20px;
border:1px solid #999;
border-top:0;
_background-image:none;
background:white;
}
.bImage {
text-align:center;
margin-top:10px;
margin-bottom:10px;
padding:10px;
border:1px;
}
</style>
<script>
function replaceScript() {
var toReplace2 = '<br>';
var replaceWith2 ='';
document.body.innerHTML = document.body.innerHTML.replace(toReplace2, replaceWith2);
var toReplace = 'Fill in at least one of the origin fields to search the gene databases.';
var replaceWith ='';
document.body.innerHTML = document.body.innerHTML.replace(toReplace, replaceWith);
}
</script>
<BODY onload="replaceScript();">
<div id="wrapper">
<div class="wpmenuspan">
<H1><img id="titlelogo" src="img/flag_lg.png"border="0"/>HVP Country Node</H1>
<span id="wpmenubloc">
<ul class="navlistop">
<li><a href="http://findis.org/index.html" class="wpmenu"><b>Home</b> </a></li>
<li><a href="http://findis.org/diseases.html" class="wpmenu"><b>Diseases</b></a></li>
<li><a href="http://findis.org/genes.html" class="wpmenu"><b>Genes</b></a></li>
<li><a href="http://findis.org/publications.html" class="wpmenu"><b>Publications</b></a></li>
<li><a href="http://findis.org/links.html" class="wpmenu"><b>Links</b></a></li>
</ul>
</span>
<!--[if IE 8]>
<style type="text/css">
.wptitle {
left: -200; /* \9 IE 8 and below */
}
</style>
<![endif]-->
<h4 class="wptitle" id="wlogotitle">
<!--[if IE 8]>
<![endif]-->
National/Ethnic Disease Database
</h4>
<!--img id="logoblock1" src="js/logoblock.png" height="" width=""/>
<img id="logoblock2" src="js/logoblock.png" height="" width=""/-->
</div>
<center>
<img src="img/blue_globe.jpeg" id="dis" height="280px" width="300px" style="position: absolute; top: -50;left: 775;">
</center>
<br/><br/><br/><br/><br/><br/>
<!--
Process query params:
gene=CHM&name=Autoimmune%20regulator&ensemb=ENSG00000160224&diseases=APECED
-->
<br/>
<table class="table table-striped table-hover table-bordered" style="width: 600px; position: relative; left:0px;" border="0" cellpadding="3" width="40%">
<tr><td style="vertical-align:middle;">
<h3><?php
$gene = isset($_GET['gene'])?$_GET['gene']:false;
if (!$gene) {
header("HTTP/1.0 400 Bad Request");
echo "Gene parameter is missing";
exit();
}
echo $gene; ?></h3>
<!-- gene name spelled out
CHROMOSOME 10 OPEN READING FRAME 2 -->
<b id="gene_info" style="font-size: 1.6em; position:relative; top:-19px;">
<?php
$name = isset($_GET['name'])?$_GET['name']:false;
if (!$name) {
header("HTTP/1.0 400 Bad Request");
echo "Name parameter is missing or malformed";
exit();
}
echo $name; ?></b>
</td><td>
<!-- Diseases associated with this gene
-->
<b id="gene_info" style="font-size: 1.1em; color: #FGFGFG;">
Diseases associated with this gene:
<?php
$disname = isset($_GET['disease'])?$_GET['disease']:false;
if (!$disname) {
header("HTTP/1.0 400 Bad Request");
echo "Disease parameter is missing";
exit();
}
$dis_url = "disease.html?disease=".$disname;
echo '<a href="'.$dis_url.'">'.$disname.'</a>';
?>
</a></b></br>
<!-- LOVD gene link -->
<b id="gene_info" style="font-size: 1.1em; color: #FGFGFG;">
LOVD Gene: <a target="_blank" style="font-size: 1em;" href="https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php?select_db=CHM&action=search_unique&order=Variant%2FDNA%2CASC&hide_col=&show_col=&limit=25&search_Variant%2FLocation=&search_Variant%2FExon=&search_Variant%2FDNA=&search_Variant%2FDNA_published=&search_Variant%2FRNA=&search_Variant%2FProtein=&search_Variant%2FInheritance=&search_Variant%2FRemarks=&search_Variant%2FReference=&search_Variant%2FHSF=&search_Variant%2FdbSNP=&search_Variant%2FUSMA=&search_Variant%2FRestriction_site=&search_Variant%2FDBID=&search_Variant%2FDNA_hg19=">CHM</a></b><br/>
<!-- NCBI gene link -->
<b id="gene_info" style="font-size: 1.1em; color: #FGFGFG;">
NCBI Gene: <a target="_blank" style="font-size: 1em;" href="http://www.ncbi.nlm.nih.gov/gene/<?php
$ncbi = isset($_GET['ncbi'])?$_GET['ncbi']:false;
echo $ncbi; ?>"><?php
$gene = isset($_GET['gene'])?$_GET['gene']:false;
echo $gene; ?></a></b><br/>
<!-- Link to Genetics Home Reference
-->
<b id="gene_info" style="font-size: 1.1em; color: #FGFGFG;">
Gene Home Reference: <a href="http://ghr.nlm.nih.gov/gene/<?php
$gene = isset($_GET['gene'])?$_GET['gene']:false;
if (!$gene) {
header("HTTP/1.0 400 Bad Request");
echo "Gene parameter is missing";
exit();
}
echo $gene; ?> " target="_blank"><?php
$gene = isset($_GET['gene'])?$_GET['gene']:false;
if (!$gene) {
header("HTTP/1.0 400 Bad Request");
echo "Gene parameter is missing";
exit();
}
echo $gene;
?></a>
</b></br>
<!-- Ensembl + OMIM links
-->
<b id="gene_info" style="font-size: 1.1em; color: #FGFGFG;">
Ensembl gene:
<?php
$ename = isset($_GET['ensemb'])?$_GET['ensemb']:false;
if (!ename) {
header("HTTP/1.0 400 Bad Request");
echo "Ensembl ID is missing";
exit();
}
$eg_url = "http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=".$ename;
echo '<a href="'.$eg_url.'" target="_blank">'.$ename.'</a>';
?>
<br/>
Ensembl location:
<?php
$ename = isset($_GET['ensemb'])?$_GET['ensemb']:false;
if (!ename) {
header("HTTP/1.0 400 Bad Request");
echo "Ensembl ID is missing";
exit();
}
$eg_url = "http://www.ensembl.org/Homo_sapiens/Location/View?g=".$ename;
echo '<a href="'.$eg_url.'" target="_blank">'.$ename.'</a>';
?></a></b><br/>
<!-- OMIM link -->
<b id="gene_info" style="font-size: 1.1em; color: #FGFGFG;">
OMIM gene:
<?php
$oname = isset($_GET['omim'])?$_GET['omim']:false;
if (!oname) {
header("HTTP/1.0 400 Bad Request");
echo "OMIM ID is missing";
exit();
}
$om_url = "http://omim.org/entry/".$oname;
echo '<a href="'.$om_url.'" target="_blank">'.$oname.'</a>';
?></a></b><br/>
<!-- External Curator Info -->
<b id="gene_info" style="font-size: 1.1em; color: #FGFGFG;">
Curator: Robert Perniola</b><br/>
<!-- Download all variants link -->
<b id="gene_info" style="font-size: 1em; color: #FGFGFG;"><a style="font-size: 1em;" href="downloads/CHM.tsv.txt">Download Finnish CHM variants</a> in tab-separated format.</b>
</td></tr>
</table>
<br/>
<h3 style="clear: left; position: relative; display: block; left:-25;"><IMG src="img/globe_blu_sm.jpeg" align="middle"/> Native Variants</h3>
<div>
<table border="0" cellpadding="0" cellspacing="1" class="data table table-striped table-hover table-bordered" style="max-width: none;">
<tbody border="0"><tr>
<th valign="top" width="50" class="order" border="0">
Path.</th>
<th valign="middle" width="80" class="order">
Location
</th>
<th valign="middle" width="50" class="order">
Exon
</th>
<th valign="top" width="200" class="order">
DNA change</th>
<th valign="top" width="104" class="order">
DNA old nomenclature</th>
<th valign="middle" width="100" class="order">
RNA change
</th>
<th valign="middle" width="200" class="order">
Protein
</th>
<th valign="middle" width="100" class="order">
Inheritance
</th>
<th valign="middle" width="200" class="order">
Variant remarks
</th>
<th valign="middle" width="150" class="order">
Reference
</th>
<th valign="middle" width="50" class="order">
HSF
</th>
<th valign="middle" width="50" class="order">
dbSNP/RFC
</th>
<th valign="middle" width="50" class="order">
Missense
</th>
<th valign="middle" width="75" class="order">
Re-site
</th>
<th valign="middle" width="200" class="order">
DB-ID
</th>
<th valign="middle" width="144" class="order">
Genomic DNA change
</th>
<th valign="middle" width="80" class="order">
Patient ID
</th>
<th valign="middle" width="200" class="order">
Disease
</th>
<th valign="middle" width="200" class="order">
Reference
</th>
<th valign="middle" width="80" class="order">
Template
</th>
<th valign="middle" width="100" class="order">
Technique
</th>
<th valign="middle" width="100" class="order">
Remarks
</th>
<th valign="middle" width="80" class="order">
# Reported
</th>
<th valign="middle" width="60" class="order">
Gender
</th>
<th valign="middle" width="136" class="order">
Geographic origin
</th>
</tr>
<tr valign="top" style="cursor : pointer; cursor : hand;" onmouseover="this.className = 'hover';" onmouseout="this.className = '';" onclick="window.location.href = 'https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php?select_db=CHM&action=view&view=0002017%2C0000139%2C0';" class="">
<td width="50">+/+</td>
<td width="80">Exon</td>
<td width="50">01-15</td>
<td width="200"><a target="_blank" href="https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php??select_db=CHM&action=view&view=0002017%2C0000139%2C0" class="data">c.-29-?_5412+?del</a></td>
<td width="104" class="order">1-?_5442+?del</td>
<td width="100">r.0</td>
<td width="200">p.0</td>
<td width="100">Hemizygous</td>
<td width="200">Total deletion of the gene. Deletion extending from DXS110 to DXS121.</td>
<td width="150"><a href="http://www.ncbi.nlm.nih.gov/pubmed/7981671" target="_blank">van Bokhoven et al., 1994</a></td>
<td width="50">-</td>
<td width="50"><a target="_blank" href="https://grenada.lumc.nl/LOVD2/Usher_montpellier/scripts/readingFrameChecker.php?mutation=del&exon_from=1&exon_to=15" target="_blank">RFC1-15</a></td>
<td width="50">-</td>
<td width="75">-</td>
<td width="200">CHM_00099</td>
<td width="144">g.85116185-?_85302565+?del</td>
<td width="80">NL010420001</td>
<td width="200">Choroideremia (CHM)</td>
<td width="200"><a href="http://www.ncbi.nlm.nih.gov/pubmed/7981671" target="_blank">van Bokhoven et al., 1994</a></td>
<td width="80">DNA</td>
<td width="100">SEQ</td>
<td width="100">-</td>
<td width="80">1</td>
<td width="60">Male</td>
<td width="136">Finland</td></tr>
<tr valign="top" style="cursor : pointer; cursor : hand;" onmouseover="this.className = 'hover';" onmouseout="this.className = '';" onclick="window.location.href = 'https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php?select_db=CHM&action=view&view=0002035%2C0000156%2C20';" class="">
<td width="50">+/+</td>
<td width="80">Exon</td>
<td width="50">09-13</td>
<td width="200"><a target="_blank" href="https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php??select_db=CHM&action=view&view=0002035%2C0000156%2C20" class="data">c.1167-?_1609+?del</a></td>
<td width="104" class="order">1197-?_1639+?del</td>
<td width="100">r.(?)</td>
<td width="200">p.(?)</td>
<td width="100">Hemizygous</td>
<td width="200">-</td>
<td width="150"><a href="http://www.ncbi.nlm.nih.gov/pubmed/2220804" target="_blank">Cremers et al., 1990</a></td>
<td width="50">-</td>
<td width="50"><a target="_blank" href="https://grenada.lumc.nl/LOVD2/Usher_montpellier/scripts/readingFrameChecker.php?mutation=del&exon_from=9&exon_to=13" target="_blank">RFC9-13</a></td>
<td width="50">-</td>
<td width="75">-</td>
<td width="200">CHM_00107</td>
<td width="144">g.85133970-?_85166343+?del</td>
<td width="80">NL010510001</td>
<td width="200">Choroideremia (CHM)</td>
<td width="200"><a href="http://www.ncbi.nlm.nih.gov/pubmed/2220804" target="_blank">Cremers et al., 1990</a></td>
<td width="80">DNA</td>
<td width="100">SEQ</td>
<td width="100">-</td>
<td width="80">1</td>
<td width="60">Male</td>
<td width="136">Finland</td></tr>
<tr valign="top" style="cursor : pointer; cursor : hand;" onmouseover="this.className = 'hover';" onmouseout="this.className = '';" onclick="window.location.href = 'https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php?select_db=CHM&action=view&view=0002045%2C0000161%2C20';" class="">
<td width="50">+/+</td>
<td width="80">Exon</td>
<td width="50">03-08</td>
<td width="200"><a target="_blank" href="https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php??select_db=CHM&action=view&view=0002045%2C0000161%2C20" class="data">c.117-?_1166+?del</a></td>
<td width="104" class="order">147-?_1196+?del</td>
<td width="100">r.(?)</td>
<td width="200">p.(?)</td>
<td width="100">Hemizygous</td>
<td width="200">-</td>
<td width="150"><a href="http://www.ncbi.nlm.nih.gov/pubmed/2220804" target="_blank">Cremers et al., 1990</a></td>
<td width="50">-</td>
<td width="50"><a target="_blank" href="https://grenada.lumc.nl/LOVD2/Usher_montpellier/scripts/readingFrameChecker.php?mutation=del&exon_from=3&exon_to=8" target="_blank">RFC3-8</a></td>
<td width="50">-</td>
<td width="75">-</td>
<td width="200">CHM_00111</td>
<td width="144">g.85211158-?_85236813+?del</td>
<td width="80">NL010480001</td>
<td width="200">Choroideremia (CHM)</td>
<td width="200"><a href="http://www.ncbi.nlm.nih.gov/pubmed/2220804" target="_blank">Cremers et al., 1990</a></td>
<td width="80">DNA</td>
<td width="100">SEQ</td>
<td width="100">-</td>
<td width="80">1</td>
<td width="60">Male</td>
<td width="136">Finland</td></tr>
<tr valign="top" style="cursor : pointer; cursor : hand;" onmouseover="this.className = 'hover';" onmouseout="this.className = '';" onclick="window.location.href = 'https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php?select_db=CHM&action=view&view=0001957%2C0000120%2C20';" class="">
<td width="50">+/+</td>
<td width="80">Intron</td>
<td width="50">13i</td>
<td width="200"><a target="_blank" href="https://grenada.lumc.nl/LOVD2/Usher_montpellier/variants.php??select_db=CHM&action=view&view=0001957%2C0000120%2C20" class="data">c.1609+2dupT</a></td>
<td width="104" class="order">1639+2_1639+3insT</td>
<td width="100">r.(?)</td>
<td width="200">p.(?)</td>
<td width="100">Hemizygous</td>
<td width="200">-</td>
<td width="150"><a href="http://www.ncbi.nlm.nih.gov/pubmed/1302003" target="_blank">Sankila et al., 1992</a> </td>
<td width="50"><a href="http://www.umd.be/HSF/4DACTION/input_SSF?choix_analyse=ssf_batch&autoselect=yes&snp_select=yes&nuclposition5=200&nuclposition3=200&choix_bdd=transcript_id&texte=ENST00000357749&batch=c.1609%2B2dupT&paramfulltables=onlyvariants&fenetreintron=yes&fenetretaille=20&paramimages=yes&showonly=no&matrice_3=yes&Matrice=PSS&Matrice=maxent&seuil_maxent5=0&seuil_maxent3=0&Matrice=BPS&Matrice=ESE finder&Matrice=RESCUE ESE&Matrice=ESE New&Matrice=Sironi&Matrice=Decamers&Matrice=ESS hnRNP&Matrice=PESE&Matrice=ESR&Matrice=EIE&seuil_sf2=72.98&seuil_sf2_esef=1.956&seuil_sf2ig=70.51&seuil_sf2ig_esef=1.867&seuil_sc35=75.05&seuil_sc35_esef=2.383&seuil_srp40=78.08&seuil_srp40_esef=2.67&seuil_srp55=73.86&seuil_srp55_esef=2.676&seuil_9g8=59.245&seuil_tra2=75.964&seuil_hnrnpa1=65.476&seuil_sironi1=60&seuil_sironi2=60&seuil_sironi3=60" target="_blank" rel="nofollow">HSF</a></td>
<td width="50">-</td>
<td width="50">-</td>
<td width="75">+MseI</td>
<td width="200">CHM_00085</td>
<td width="144">g.85133968dup</td>
<td width="80">NL010310001</td>
<td width="200">Choroideremia (CHM)</td>
<td width="200"><a href="http://www.ncbi.nlm.nih.gov/pubmed/1302003" target="_blank">Sankila et al., 1992</a> </td>
<td width="80">DNA</td>
<td width="100">SSCA</td>
<td width="100">-</td>
<td width="80">1</td>
<td width="60">Male</td>
<td width="136">FINLAND</td></tr></tbody></table>
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