c4107b587391b4757477c10fb6cb0df022d854fb
kuhn
  Wed Feb 26 14:05:10 2020 -0800
put color information for SNPs in color to catch the eye

diff --git src/hg/makeDb/trackDb/human/dbSnp153Composite.html src/hg/makeDb/trackDb/human/dbSnp153Composite.html
index 1b430a2..651ba9b 100644
--- src/hg/makeDb/trackDb/human/dbSnp153Composite.html
+++ src/hg/makeDb/trackDb/human/dbSnp153Composite.html
@@ -75,37 +75,40 @@
 individuals have "TAAG" at the same location, then the variant is a deletion of a single
 A relative to the reference genome.
 However, which A was deleted?  There is no way to tell whether the first, second or third A
 was removed.
 Different variant mapping tools may place the deletion at different bases in the reference genome.
 In order to reduce errors in merging variant calls made with different left vs. right biases,
 dbSNP made a major change in its representation of deletion/insertion variants in build 152.
 Now, instead of assigning a single-base genomic location at one of the A's,
 dbSNP expands the coordinates to encompass the whole repetitive region,
 so the variant is represented as a deletion of 3 A's combined with an insertion of 2 A's.
 In the track display, there will be a half-height box covering the first two A's,
 followed by a full-height box covering the third A, in order to show a net loss of one base
 but an uncertain placement within the three A's.
 </p>
 <p>
-Variants are colored according to functional effect on genes annotated by dbSNP.
-Protein-altering variants and splice site variants are
-red,
-synonymous codon variants are
-green,
-and non-coding transcript or Untranslated Region (UTR) variants are
-blue.
+Variants are colored according to functional effect on genes annotated by dbSNP:
+</p>
+
+<p><b><font color=red>Protein-altering variants and splice site variants are
+red</font></b>.
+<br><b><font color=green>Synonymous codon variants are
+green</font></b>.
+<br><b><font color=blue>
+Non-coding transcript or Untranslated Region (UTR) variants are
+blue</font></b>.
 </p>
 <p>
 On the track controls page, several variant properties can be included or excluded from
 the item labels:
 rs# identifier assigned by dbSNP,
 reference/alternate alleles,
 major/minor alleles (when available) and
 minor allele frequency (when available).
 Allele frequencies are reported independently by twelve projects
 (some of which may have overlapping sets of samples):
   <ul>
     <li><a href="https://www.internationalgenome.org/" target=_blank>1000Genomes</a>:
       The 1000 Genomes Phase 3 dataset contains data for 2,504 individuals from 26 populations.
     </li>
     <li><a href="https://gnomad.broadinstitute.org/" target=_blank>GnomAD exomes</a>: