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yet</button><a id="jr-fip-next" class="wsprkl btn" title="Jump to next match">▶</a></nav></nav></div><div id="jr-epub-interstitial" class="hidden"></div><div id="jr-content"><article data-type="main"><p class="vip-notice retraction"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p><div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><div class="fm-sec"><h1 id="_NBK573453_"><span class="title" itemprop="name">Field Definitions</span></h1><p class="fm-aai"><a href="#_NBK573453_pubdet_">Publication Details</a></p><p><em>Estimated reading time: 2 minutes</em></p></div></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><ul class="simple-list"><li><p><a href="#Schm_Field_Definitio.can_you_direct_me_t">Can you direct me to the correct file that provides detailed definitions for primary keys and table fields?</a></p></li><li><p><a href="#Schm_Field_Definitio.what_is_the_field_d">What is the field definition for the refSNP number?</a></p></li><li><p><a href="#Schm_Field_Definitio.what_are_the_defini">What are the definitions of contig_chr, contig_pos, and contig_build_id?</a></p></li><li><p><a href="#Schm_Field_Definitio.what_is_the_definit">What is the definition of "contig_pos=0"?</a></p></li><ul class="simple-list"><li><h4>SNPAncestralAllele table</h4></li><li><p><a href="#Schm_Field_Definitio.what_is_the_definit_1">What is the definition for the ancestral_allele_id field located in the SNPAncestralAllele table? If the ancestral_allele_id is equal to 7, what does the id represent?</a></p></li><li><p><a href="#Schm_Field_Definitio.does_the_ancestral">Does the "ancestral_allele_id" column in the "SNPAncestralAllele" table refer to the "univar_id" column in the"UniVariation" table?</a></p></li><li><p><a href="#Schm_Field_Definitio.i_want_the_ancestra">I want the ancestral allele for a number of rsIDs, but can’t find rsID numbers in Allele.bcp.gz and SNPAncestralAllele.bcp.gz.</a></p></li></ul><ul class="simple-list"><li><h4>SNPChrPosOnRef</h4></li><li><p><a href="#Schm_Field_Definitio.what_does_what_does">What does what does orient=0 and orient=1 represent in the "orient" column of the SNPChrPosOnRef table?</a></p></li></ul><ul class="simple-list"><li><h4>SNPContigLocusId table</h4></li><li><p><a href="#Schm_Field_Definitio.how_do_i_determine">How do I determine to the refSNP (rs) ID for the snpID in theSNPContigLocusId.bcp.gz file?</a></p></li><li><p><a href="#Schm_Field_Definitio.is_snp_location_cod">Is SNP location (coding region, splice site or promoter region) stored in the fxn_class field of the SNPContigLocusId table? If so, where is the corresponding function class for promoter region?</a></p></li></ul><ul class="simple-list"><li><h4>SubInd table</h4></li><li><p><a href="#Schm_Field_Definitio.where_can_i_find_th">Where can I find the definition for the submitted_strand_code column that is located in the SubInd table?</a></p></li></ul></ul><div><h4 id="Schm_Field_Definitio.can_you_direct_me_t">Can you direct me to the correct file that provides detailed definitions for primary keys and table fields?</h4><blockquote><p>Most table field descriptions are still valid and are located in the <a href="ftp://ftp.ncbi.nlm.nih.gov/snp/database/b124/mssql/schema/DataDictionary_b118.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">Data Dictionary</a>. Changes to the tables in each build are listed in the <a href="/SNP/snp_schemaChange.htm" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Schema Change document</a>. <b>(3/28/05)</b></p></blockquote></div><div><h4 id="Schm_Field_Definitio.what_is_the_field_d">What is the field definition for the refSNP number?</h4><blockquote><p>dbSNP stores the refSNP number as an integer (a big integer) <b>(7/6/05)</b>.</p></blockquote></div><div><h4 id="Schm_Field_Definitio.what_are_the_defini">What are the definitions of contig_chr, contig_pos, and contig_build_id?</h4><blockquote><p>contig_chr is the chromosome for this SNP (if known).<br />contig_pos is the position on the chromosome.<br />contig_build_id is the build in which the SNP was last edited.</p></blockquote></div><div><h4 id="Schm_Field_Definitio.what_is_the_definit">What is the definition of "contig_pos=0"?</h4><blockquote><p>This is a case in which the SNP has not been mapped to the human genome<br />reference sequence.</p></blockquote></div><div id="Schm_Field_Definitio.SNPAncestralAllele"><h2 id="_Schm_Field_Definitio_SNPAncestralAllele_">SNPAncestralAllele table</h2><div><h4 id="Schm_Field_Definitio.what_is_the_definit_1">What is the definition for the ancestral_allele_id field located in the SNPAncestralAllele table? If the ancestral_allele_id is equal to 7, what does the id represent?</h4><blockquote><p>SNPAncestralAllel.ancestral_allele_id refers to Allele.allele_id.</p><p>If ancestral_allele_id = 7, select allele from Allele where allele_id =7 gets "C".<b>(3/7/05)</b></p></blockquote></div><div><h4 id="Schm_Field_Definitio.does_the_ancestral">Does the "ancestral_allele_id" column in the "SNPAncestralAllele" table refer to the "univar_id" column in the"UniVariation" table?</h4><blockquote><p>You are on the right track: "ancestral_allele_id" refers to table Allele.</p><p>Please note that "ancestral allele" refers to the allele state in ancestral chromosomes. "ancestral allele" does not contain variation information in itself. UniVariation lists at least two alleles (A/G). (<b>01/23/08</b>)</p></blockquote></div><div><h4 id="Schm_Field_Definitio.i_want_the_ancestra">I want the ancestral allele for a number of rsIDs, but can’t find rsID numbers in Allele.bcp.gz and SNPAncestralAllele.bcp.gz.</h4><blockquote><p>If you go to the dbSNP Data Dictionary and search for “<a href="/projects/SNP/snp_db_table_description.cgi?t=SNPAncestralAllele" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">SNPAncestralAllele</a>”, you’ll find that the rsID is stored as an integer in the first column of the table.</p><p>Here’s an example to help you — say you want to find the ancestral allele for <a href="/snp/?term=3" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=snp">rs3</a>:</p><dl class="temp-labeled-list"><dl class="bkr_refwrap"><dt>1.</dt><dd><p class="no_top_margin">Look for the number “3” in first column of the SNPAncestralAllele table and you’ll find that the corresponding ancestral allele ID (located in the second column) is 7.</p></dd></dl><dl class="bkr_refwrap"><dt>2.</dt><dd><p class="no_top_margin">Now, look in the Allele table for the allele letter that corresponds to<br />Ancestral allele ID = 7. In the allele table, the allele ID number is again located in the first column:<br /><br />7 C 2003-02-22 01:11:00.0 2 2003-10-06 17:42:00.0</p></dd></dl></dl><p>So you can see from this example, that the ancestral allele for <a href="/snp/?term=3" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=snp">rs3</a> is “C”. (<b>08/29/08</b>)</p></blockquote></div></div><div id="Schm_Field_Definitio.SNPChrPosOnRef"><h2 id="_Schm_Field_Definitio_SNPChrPosOnRef_">SNPChrPosOnRef</h2><div><h4 id="Schm_Field_Definitio.what_does_what_does">What does what does orient=0 and orient=1 represent in the "orient" column of the SNPChrPosOnRef table?</h4><blockquote><p>Orient=0 means that the SNP is in the same orientation as the chromosome. Orient=1 means that the SNP is in the opposite orientation as the chromosome. (<b>01/03/08</b>)</p></blockquote></div></div><div id="Schm_Field_Definitio.SNPContigLocusId_ta"><h2 id="_Schm_Field_Definitio_SNPContigLocusId_ta_">SNPContigLocusId table</h2><div><h4 id="Schm_Field_Definitio.how_do_i_determine">How do I determine to the refSNP (rs) ID for the snpID in theSNPContigLocusId.bcp.gz file?</h4><blockquote><p>The refSNP (rs) ID <b>is</b>
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<b>the ID</b> number given in the "snp_id" field of the SNPContigLocusId.bcp.gz in file. You can confirm this by doing the following:</p><p>Look at the rs number associated with a gene on a refSNP page. For example, go to the refSNP cluster report for <a href="/snp/?term=268" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=snp">rs268</a>. If you look at the very top of the “Geneview” section of this report, you will see that the SNP is associated with the LPL gene (Lipoprotein Lipase). If you click on the “LPL” link at the top of “Geneview” section, you will get a <a href="/sites/entrez?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=4023" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Entrez Gene report for LPL</a>, which states that the gene ID for LPL is 4023.</p><p>Now, if you go to the SNPContigLocusId.bcp file, you will see a row that contains snp_id 268. That same row will have gene_id 4023.</p><p>I should mention that you will see two rows for <a href="/snp/?term=268" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=snp">rs268</a>, one representing the reference contig, and one representing the Celera contig. (<b>11/19/07</b>)</p></blockquote></div><div><h4 id="Schm_Field_Definitio.is_snp_location_cod">Is SNP location (coding region, splice site or promoter region) stored in the fxn_class field of the SNPContigLocusId table? If so, where is the corresponding function class for promoter region?</h4><blockquote><p>Yes, the location information for SNPs are in the the fxn_class field of the SNPContigLocusId table, but I don't think that the current snp function class set includes "promoter region".</p></blockquote></div></div><div id="Schm_Field_Definitio.SubInd_table"><h2 id="_Schm_Field_Definitio_SubInd_table_">SubInd table</h2><div><h4 id="Schm_Field_Definitio.where_can_i_find_th">Where can I find the definition for the submitted_strand_code column that is located in the SubInd table?</h4><blockquote><p>You can <a href="/SNP/snp_db_list_table.cgi?fld=ColumnName&cond=conains&srch=submitted_strand_code&srch=&cond=&type=&fld=&go=Search+%28case+insensitive%29&.cgifields=cond&.cgifields=fld(4/28/06)" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">search</a> for the column definition using the online database dictionary. (<b>4/28/06</b>)</p></blockquote></div></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK573453_pubdet_">Publication Details</h2><h3>Publication History</h3><p class="small">Created: <span itemprop="datePublished">August 8, 2005</span>; Last Update: <span itemprop="dateModified">June 15, 2010</span>.</p><h3>Copyright</h3><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div></div><h3>Publisher</h3><p><a href="http://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>, Bethesda (MD)</p><h3>NLM Citation</h3><p>SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-. Field Definitions. 2005 Aug 8 [Updated 2010 Jun 15].<span class="bk_cite_avail"></span></p></div><div class="small-screen-prev"><a href="/books/n/helpsnpfaq/Schm_SchemaTable_Def/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M75,30 c-80,60 -80,0 0,60 c-30,-60 -30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Prev</text></svg></a></div><div class="small-screen-next"><a href="/books/n/helpsnpfaq/Schm_Schema_Changes_/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M25,30c80,60 80,0 0,60 c30,-60 30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Next</text></svg></a></div></article></div><div id="jr-scripts"><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/libs.min.js"> </script><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.min.js"> </script></div></div>
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