dd48ec1870d25c306ac3cb7d02849566050fc44d
abenetpa
  Wed Sep 30 07:50:29 2020 -0700
listed variant color conventions

diff --git src/hg/makeDb/trackDb/human/clinvar.html src/hg/makeDb/trackDb/human/clinvar.html
index 8edd0f6..f159e94 100644
--- src/hg/makeDb/trackDb/human/clinvar.html
+++ src/hg/makeDb/trackDb/human/clinvar.html
@@ -33,48 +33,52 @@
 However, be aware that the ClinVar conventions are different from the VCF standard. 
 Variants may be right-aligned or may contain additional context, e.g. for
 inserts. ExAC/gnomAD make available <a href="https://github.com/macarthur-lab/clinvar"
 target="_blank">a converter</a>
 to make ClinVar more comparable to VCF files.</p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 The genomic locations of ClinVar variants are labelled with the ClinVar variant descriptions. 
 <b>Mouseover</b> on items shows variant details, clinical interpretation, and associated conditions. 
 Further information on each variant is displayed on the details page by a click onto any variant.
 </p>
 
 <p>
-Entries in the <b>ClinVar CNVs track</b> are colored by <b>type of variant</b>, among others,
-<b><font color="red">red for loss</font></b>,
-<b><font color="blue">blue for gain</font></b>,
-<b><font color="purple">purple for inversion</font></b>, and
-<b><font color="orange">orange for insertion</font></b>.
+Entries in the <b>ClinVar CNVs track</b> are colored by <b>type of variant</b>, among others:
+<ul>
+ <li><b><font color="red">red for loss</font></b></li>
+ <li><b><font color="blue">blue for gain</font></b></li>
+ <li><b><font color="purple">purple for inversion</font></b></li>
+ <li><b><font color="orange">orange for insertion</font></b></li>
+</ul>
 A light-to-dark color gradient indicates the <b>clinical significance</b> of each variant, with the 
 lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the 
 CNV color code is described 
 <a href="https://genome.ucsc.edu/goldenPath/help/hgCnvColoring.html">here</a>. 
 </p>
 
 <p>
 Entries in the <b>ClinVar SNVs track</b> are colored by <b>clinical significance</b>:
-<b><font color="d20000">red for pathogenic</font></b>,
-<b><font color="000088">dark blue for variant of uncertain significance</font></b>,
-<B><font color="#00d200">green for benign</font></b>,
-<B><font color="#888">dark grey for not provided</font></b>, and
-<B><font color="#8979D4">light blue for conflicting</font></b>.
+<ul>
+ <li><b><font color="d20000">red for pathogenic</font></b></li>
+ <li><b><font color="000088">dark blue for variant of uncertain significance</font></b></li>
+ <li><B><font color="#00d200">green for benign</font></b></li>
+ <li><B><font color="#888">dark grey for not provided</font></b></li>
+ <li><B><font color="#8979D4">light blue for conflicting</font></b></li>
+</ul>
 </p>
 
 <p>
 Items can be filtered according to the size of the variant, variant type, clinical significance, 
 allele origin, and molecular consequence, using the track <b>Configure</b> options. 
 Each subtrack has separate display controls, as described 
 <a href="https://genome.ucsc.edu/goldenPath/help/multiView.html">here</a>.
 
 <p>For the human genome version hg19: the hg19 genome released by UCSC in 2009 had a 
 mitochondrial genome "chrM" that was not the same as the one later used for most
 databases like ClinVar. As a result, we added the official mitochondrial genome
 in 2020 as "chrMT" and all mitochondrial annotations of ClinVar and most other
 databases are shown on the mitochondrial genome called "chrMT". For full description
 of the issue of the mitochondrial genome in hg19, please see the 
 <a target=_blank href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/">README file</a>