c15e02af297b6d6f82492bb6a370225cebe15f67 dschmelt Wed Dec 23 17:00:55 2020 -0800 Releasing the highly anticipated COVID GWAS v4 refs #26616 diff --git src/hg/makeDb/trackDb/human/covidHgiGwasR4Pval.html src/hg/makeDb/trackDb/human/covidHgiGwasR4Pval.html index 81e5569..975c1e2 100644 --- src/hg/makeDb/trackDb/human/covidHgiGwasR4Pval.html +++ src/hg/makeDb/trackDb/human/covidHgiGwasR4Pval.html @@ -31,67 +31,59 @@ for COVID-19 vs. population (i.e. everybody that is not a case). The increased sample size resulted in strong evidence of seven genomic regions associated with severe COVID-19 and one additional signal associated with COVID-19 partial-susceptibility. Many of these regions were identified by the <a target="_blank" href="https://genomicc.org/">Genetics of Mortality in Critical Care (GenOMICC)</a> study and are shown below (table adapted from <a target="_blank" href="https://www.nature.com/articles/s41586-020-03065-y">Pairo-Castineira <em>et. al.</em></a>). </li> <p></p> <table class="stdTbl"> <tr> <th>SNP</th> <th>Human GRCh37/hg19 Assembly</th> <th>Human GRCh38/hg38 Assembly</th> - <th>Risk Alelle</th> + <th>Risk Allele</th> <th>Alternative</th> <th>Gene nearest to SNP</th> </tr> <tr> <td>rs73064425</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr3:45901089-45901089">chr3:45901089-45901089</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr3:45859597-45859597">chr3:45859597-45859597</a></td> <td>T</td> <td>C</td> <td>LZTFL1</td> </tr> <tr> <td>rs9380142</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr6:29798794-29798794">chr6:29798794-29798794</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr6:29831017-29831017">chr6:29831017-29831017</a></td> <td>A</td> <td>G</td> <td>HLA-G</td> </tr> <tr> <td>rs143334143</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr6:31121426-31121426">chr6:31121426-31121426</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr6:31153649-31153649">chr6:31153649-31153649</a></td> <td>A</td> <td>G</td> <td>CCHCR1</td> </tr> <tr> - <td>rs3131294</td> - <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr6:32180146-32180146">chr6:32180146-32180146</a></td> - <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr6:32212369-32212369">chr6:32212369-32212369</a></td> - <td>G</td> - <td>A</td> - <td>NOTCH4</td> - </tr> - <tr> <td>rs10735079</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr12:113380008-113380008">chr12:113380008-113380008</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr12:112942203-112942203">chr12:112942203-112942203</a></td> <td>A</td> <td>G</td> <td>OAS3</td> </tr> <tr> <td>rs74956615</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr19:10427721-10427721">chr19:10427721-10427721</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr19:10317045-10317045">chr19:10317045-10317045</a></td> <td>A</td> <td>T</td> <td>ICAM5/TYK2</td> </tr> @@ -107,36 +99,36 @@ <td>rs2236757</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr21:34624917-34624917">chr21:34624917-34624917</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr21:33252612-33252612">chr21:33252612-33252612</a></td> <td>A</td> <td>G</td> <td>IFNAR2</td> </tr> </table> </p> <p> <li><b>Hosp COVID vars (B2):</b> Cases hospitalized and confirmed for COVID-19 vs. population (i.e. everybody that is not a case)</li> </p> <p> <li><b>Tested COVID vars (C1):</b> Cases with laboratory confirmed SARS-CoV-2 infection, or -health record/phisician-confirmed COVID-19, or self-reported COVID-19 via questionare vs. laboratory +health record/physician-confirmed COVID-19, or self-reported COVID-19 via questionare vs. laboratory /self-reported negative cases</li> </p> <p> <li><b>All COVID vars (C2):</b> Cases with laboratory confirmed SARS-CoV-2 infection, or -health record/phisician-confirmed COVID-19, or self-reported COVID-19 vs. population (i.e. everybody +health record/physician-confirmed COVID-19, or self-reported COVID-19 vs. population (i.e. everybody that is not a case)</li> </p> </ul> Due to privacy concerns, these browser tracks exclude data provided by 23andMe contributed studies in the full analysis results. The actual study and case and control counts for the individual browser tracks are listed in the track labels. Details on all studies can be found <a target="=blank" href="https://www.covid19hg.org/results/">here</a>. <H2>Display Conventions</H2> <p> Displayed items are colored by <b>GWAS effect</b>: red for positive (harmful) effect, blue for negative (protective) effect. The height ('lollipop stem') of the item is based on statistical significance (<b>p-value</b>). For better visualization of the data, only SNPs with p-values smaller than 1e-3 are