577 lines
36 KiB
HTML
577 lines
36 KiB
HTML
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<meta name='referrer' content='origin-when-cross-origin'/><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4198063/css/4121862/3974050/3917732/251717/4186383/14534/45193/3534283/4128070/2867781/3621797/4005757.css" /><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4198063/css/3529741/3529739.css" media="print" /><script type="text/javascript">
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<strong>Warning:</strong>
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The NCBI web site requires JavaScript to function.
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<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
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<a id="nws_header_accesskey_0" href="https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys" class="usa-sr-only" accesskey="0" tabindex="-1">Access keys</a>
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<a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a>
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<a id="nws_header_accesskey_2" href="/myncbi/" class="set-base-url usa-sr-only" accesskey="2" tabindex="-1">MyNCBI Homepage</a>
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<a id="nws_header_accesskey_3" href="#maincontent" class="usa-sr-only" accesskey="3" tabindex="-1">Main Content</a>
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<!--/.header-->
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<div class="header">
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<div class="res_logo"><h1 class="res_name"><a href="/variation/" title="Medical Genetics and Human Variation home">Medical Genetics and Human Variation</a></h1><h2 class="res_tagline">Tagline for the app</h2></div>
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<form class="search_form" action="/gquery/" method="get">
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<label for="searchbarlite">Search NCBI </label>
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<input class="jig-ncbiclearbutton" type="text" size="40" id="searchbarlite" name="term" />
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<button type="submit" id="search" class="button_search">Search</button>
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<style type="text/css"></style>
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<input type="hidden" name="p$a" id="p$a" /><input type="hidden" name="p$l" id="p$l" value="PAFAppLayout" /><input type="hidden" name="p$st" id="p$st" value="variation" /><input name="SessionId" id="SessionId" value="CE8BC1E97D9F05E1_0182SID" disabled="disabled" type="hidden" /><input name="Snapshot" id="Snapshot" value="/projects/variation/variation@1.9" disabled="disabled" type="hidden" /></form>
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</div>
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<div class="nav_and_browser">
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</div>
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<!-- was itemctrl -->
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<h2 id="resource-summary">Resource Summary</h2>
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<p><table border="1" cellpadding="1" cellspacing="1">
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<thead>
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<tr>
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<th scope="col">Name</th>
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<th scope="col">Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>
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<a href="/clinvar/">ClinVar</a>
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</td>
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<td>Reported relationships between human variation and observed health status with supporting evidence</td>
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</tr>
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<tr>
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<td>
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<a href="/snp/">dbSNP</a>
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</td>
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<td>Single nucleotide variations, microsatellites, small-scale insertions and deletions, and population-specific frequencies</td>
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</tr>
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<tr>
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<td>
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<a href="/dbvar/">dbVar</a>
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</td>
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<td>Large scale genomic variation, including large insertions, deletions, translocations, and inversions</td>
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</tr>
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<tr>
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<td>
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<a href="/gtr/">GTR®<a>
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</a></a></td>
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<td>Genetic tests and laboratories,with detailed information about the tests such as what is measured and analytic and clinical validity</td>
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</tr>
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<tr>
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<td>
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<a href="/gap/">dbGaP</a>
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</td>
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<td>Genome-wide association (GWAS) and other studies which investigate the interaction of genotype and phenotype</td>
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</tr>
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<tr>
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<td>
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<a href="/gap/phegeni/">PheGenI</a>
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</td>
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<td>Search for human phenotype genotype relationships</td>
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</tr>
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<tr>
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<td>
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<a href="/medgen/">MedGen</a>
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</td>
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<td>An aggregator of terms from multiple, authoritative sources on genetic diseases and conditions, organized into concept groupings and hierarchies</td>
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</tr>
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<tr>
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<td>
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<a href="/books/NBK1116/">GeneReviews®<a>
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</a></a></td>
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<td>Expert-authored, peer-reviewed disease descriptions that apply genetic testing to the diagnosis and management of inherited conditions</td>
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</tr>
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<tr>
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<td>
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<a href="/books/NBK61999/">Medical Genetics Summaries (MGS)</a>
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</td>
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<td>Summaries reviewing genetic variants that underlie inherited conditions, disesase risk, and specific drug responses</td>
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</tr>
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<tr>
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<td>
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<a href="/variation/view/">Variation Viewer</a>
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</td>
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<td>A genomic browser for variations by chromosomal location, gene symbol, phenotype, or variant IDs from dbSNP, dbVar, and ClinVar</td>
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</tr>
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<tr>
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<td>
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<a href="/osiris/">OSIRIS</a>
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</td>
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<td>Quality assurance software package to analyze multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols</td>
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</tr>
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</tbody>
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</table>
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</p>
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<h2 id="which-tool-do-i-use-for-">Which tool do I use for .... ?</h2>
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<ol>
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<li>I have 3000 variant calls. How do I find out which is possibly significant? - Use <a href="/variation/services">Variation Services</a>.</li>
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<li>I am studying my favorite gene. How do I find all variants on that gene? - Use <a href="/variation/view">Variation Viewer</a>.</li>
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<li>I have a VCF file in GRCh37 coordinates. How do I move those to GRCh38 coordinates? - Use the <a href="/genome/tools/remap#tab=rsg"><span data-scaytid="189" word="NCBI"> NCBI </span> <span data-scaytid="191" word="Remap"> Genome Remapping </span> Service.</a></li>
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<li>I want to search the NHGRI GWAS Catalog for studies related to Basal Cell Carcinoma. - Use <a href="/gap/phegeni">PheGenI</a>.</li>
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<li>I want to access the database for small or large structural variations. - Refer to <a href="/variation/dbSNP_dbVar_FAQ/">dbSNP and dbVar FAQs</a>.</li>
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</ol>
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<p><span id="Tools"></span></p>
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<h2 id="-ncbi-variation-tools-"><span> NCBI Variation Tools </span></h2>
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<p><span> This is a list of available NCBI Variation Tools for investigating and understanding human variation. </span></p>
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<h3 id="-variation-services-"><span> <a href=""></a> Variation Services </span></h3>
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<p><a href="/variation/services">Variation Services</a> is an API for processing medium volume of data (<100K variants). It has functions for searching, normalizing, remapping, and annotating user's variants with dbSNP data.
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Users that need a high volume of data (>100K variants) can access the dbSNP by <a href="https://ftp.ncbi.nih.gov/snp/redesign/latest_release/">FTP</a>.</p>
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<h3 id="-variation-viewer-"><span> <a href=""></a> Variation Viewer </span></h3>
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<p><a href="/variation/view">Variation Viewer</a> is a tool for interactive examination and download of nucleotide variants for a specific locus. It supports both the <span data-scaytid="171" word="GRCh38"> GRCh38 </span> and GRCh37.p13 assemblies. Variation Viewer integrates data from all of the <span data-scaytid="172" word="NCBI"> NCBI </span> Variation databases and presents them in a coupled graphical and tabular report. The resulting list of variants can be saved locally using the download function. You can also upload their own variant data to this browser. More information can be found on the <a href="ftp://ftp/pub/factsheets/Factsheet_Variation_Viewer.pdf"><span data-scaytid="173" word="NCBI"> NCBI </span> Variation Viewer Fact sheet</a> and in an <a href="https://www.youtube.com/watch?v=rnWZ9MFBwUM">introductory video tutorial</a>.</p>
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<h3 id="-ncbi-genome-remapping-service-"><span> <a href=""></a> NCBI Genome Remapping Service </span></h3>
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<p>The <a href="/genome/tools/remap#tab=rsg"><span data-scaytid="189" word="NCBI"> NCBI </span> <span data-scaytid="191" word="Remap"> Genome Remapping </span> Service</a> is a tool that projects users' annotation data from one coordinate system to another. With the Assembly-Assembly remap, you can remap your variant calls between different assembly versions, while the Clinical Remap permits you to remap data between RefSeqGenes or LRGs and an assembly, using NCBI calculated alignments. More information can be found on the <a href="ftp://ftp/pub/factsheets/Factsheet_Remap.pdf"><span data-scaytid="194" word="NCBI"> NCBI </span> <span data-scaytid="195" word="Remap"> Remap </span> Service fact sheet</a>. The remapping service has a web interface as well as an <a href="/genome/tools/remap/docs/api">API</a> for bulk processing.</p>
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<h3 id="-phegeni-"><span> <a href=""></a> PheGenI </span></h3>
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<p>The Phenotype-Genotype Integrator (<a href="/gap/phegeni"><span data-scaytid="143" word="PheGenI">PheGenI</span></a>) is a tool that integrates the search and retrieval of associated genotype-phenotype data from National Human Genome Research Institute (NHGRI) Genome-wide Association Study (GWAS) Catalog integrated with data housed in Gene, dbGaP, OMIM, GTEx and dbSNP. It provides search by genotype and phenotype. The dbSNP Data in NCBI PheGenI is only mapped GRCh38 at this time. More information can be found on the <a href="ftp://ftp/pub/factsheets/Factsheet_PheGenI.pdf"><span data-scaytid="194" word="NCBI"> NCBI </span> Phenotype-Genotype Integrator fact sheet.</a></p>
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<ul class="mt-3">
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<li>
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<a class="text-white" href="//www.nlm.nih.gov/">NLM</a>
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</li>
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<li>
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<a class="text-white" href="https://www.nih.gov/">NIH</a>
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</li>
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<li>
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<a class="text-white" href="https://www.hhs.gov/">HHS</a>
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</li>
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<li>
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<a class="text-white" href="https://www.usa.gov/">USA.gov</a>
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</li>
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</section>
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<script type="text/javascript" src="/portal/portal3rc.fcgi/static/js/hfjs2.js"> </script>
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<p class="last-updated small">Last updated: 2021-11-03T18:41:23Z</p>
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<span class="PAFAppResources"></span>
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</div><!-- /.twelve_col -->
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<span class="pagefixtures"></span>
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</html>
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