089c09e98db52e92da694ab1a0c8891c1a7fd3e8
gperez2
  Thu Apr 2 15:50:07 2026 -0700
Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run).

Updated 261 trackDb HTML and .ra files:
- Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs,
chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations;
removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download,
oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs).
- Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com,
drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains
(blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix);
removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com).
- Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org,
cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org,
hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path).

No RM.

diff --git src/hg/makeDb/trackDb/human/geneHancer.html src/hg/makeDb/trackDb/human/geneHancer.html
index eae6d75cec9..419acdc1a09 100644
--- src/hg/makeDb/trackDb/human/geneHancer.html
+++ src/hg/makeDb/trackDb/human/geneHancer.html
@@ -77,31 +77,31 @@
 Clusters composed of interactions with a single gene are colored to correspond to the gene, 
 and those composed of interactions with multiple genes are colored dark gray.</p>
 
 <h2>Methods</h2> 
 <p>
 GeneHancer identifications were created from &gt;1 million regulatory elements 
 obtained from seven genome-wide databases:
 <ol>
 <li><a href="https://www.encodeproject.org/" target="_blank">ENCODE project</a>
 <a href="http://zlab-annotations.umassmed.edu/enhancers/" target="_blank">Z-Lab Enhancer-like regions</a> (version v3)</li>
 <li><a href="https://useast.ensembl.org/info/genome/funcgen/index.html" target="_blank">Ensembl regulatory build</a> (version 92)</li>
 <li><a href="https://fantom.gsc.riken.jp/" target="_blank">FANTOM5</a><a href="https://pressto.binf.ku.dk/"
 
                                                                                  target="_blank"> atlas of active enhancers</a></li>
 <li><a href="https://enhancer.lbl.gov/" target="_blank">VISTA Enhancer Browser</a></li>
-<li><a href="http://asntech.org/dbsuper/" target="_blank">dbSUPER super-enhancers</a></li>
+<li><a href="https://asntech.org/dbsuper/" target="_blank">dbSUPER super-enhancers</a></li>
 <li><a href="https://epd.vital-it.ch/EPDnew_database.php" target="_blank">EPDnew promoters</a></li>
 <li><a href="https://ccg.vital-it.ch/UCNEbase/" target="_blank">UCNEbase ultra-conserved noncoding elements</a></li>
 </ol>
 <p>
 Employing an integration algorithm that removes redundancy, the GeneHancer pipeline
 identified &tilde;250k integrated candidate regulatory elements (GeneHancers).
 Each GeneHancer is assigned an annotation-derived confidence score. 
 The GeneHancers that are derived from more than one information source are defined 
 as &quot;elite&quot; GeneHancers.</p>
 <p>
 Gene-GeneHancer associations, and their likelihood-based scores, were generated 
 using information that helps link regulatory elements to genes:
 <ol>
 <li>eQTLs (expression quantitative trait loci) from <a href="https://www.gtexportal.org/home/" 
 target="_blank">GTEx</a> (version v6p)</li>