<?xml version='1.0'?> <pml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="pml.xsd" > <source uid="IMS-JST" id="1" db="JSNP" name="Yusuke Nakamura" laboratory="of Human Genome Center(HGC), Institute of Medical Science(IMS), The University of Tokyo and the Japan Science and Technology Agency(JST). " /> <distributor uid="IMS-JST" name="JSNP" db="JSNP" id="2" lsid="urn:lsid:ims.u-tokyo.ac.jp:JSNP:IMS-JST"> <db_xref db="JSNP" uid="IMS-JST" url="http://snp.ims.u-tokyo.ac.jp/" /> </distributor> <panel id="3" lsid="urn:lsid:ims.u-tokyo.ac.jp:JSNP:IMS-JST" size="48" count_unit="chromosome" ethnicity="japanese" > <annotation name="description" value="24 unrelated Japanese volunteers" /> <taxon id="100" scientific_name="Homo sapience"> <db_xref db="Unified Taxonomy Database" uid="9606" /> </taxon> </panel> <molecular_sample molecule="Genomic" id="4"> <polymorphism_assay id="5" /> <panel id="3" /> </molecular_sample> <polymorphism_assay id="5" lsid="urn:lsid:ims.u-tokyo.ac.jp:JSNP:m1"> <db_xref db="JSNP" uid="m1" url="http://snp.ims.u-tokyo.ac.jp/samplesMethods.html" /> <annotation name="description" value="Direct sequencing" /> <genomic_polymorphism id="9" /> </polymorphism_assay> <assayed_genomic_genotype id="6"> <genomic_allele id="7" sequence="A" /> <genomic_allele id="8" sequence="G" /> <polymorphism_assay id="5" /> <molecular_sample id="4" /> </assayed_genomic_genotype> <genomic_polymorphism flank_up="TGACCCCTCT GTGTTCACCT ACTCTGCTCT CAGCCCCACC TTGTCTCTCC AGTGCAGATC" flank_down="GCCTGCCCTC CACCATGCGC ATGACAGTGG CTGACGGCAC TGTATACATA GCCCAGCAGA" id="9" lsid="urn:lsid:ims.u-tokyo.ac.jp:JSNP:IMS-JST070162"> <db_xref db="JSNP" uid="IMS-JST070162" url="http://snp.ims.u-tokyo.ac.jp/cgi-bin/SnpInfo.cgi?SNP_ID=IMS-JST070162" /> <db_xref db="dbSNP" uid="ss3210078" url="http://www.ncbi.nih.gov/SNP/snp_retrieve.cgi?subsnp_id=ss3210078" /> <db_xref db="dbSNP" uid="rs2274333" url="http://www.ncbi.nih.gov/SNP/snp_ref.cgi?rs=rs2274333" /> <reference_genomic_location_in_assembly start="8951470" end="8951470" strand="1" chromosome_name="1"> <reference_genomic_assembly name="NCBI Build" version="35.1" /> </reference_genomic_location_in_assembly> <reference_genomic_location start="3554571" end="3554571" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> <genomic_allele id="7" sequence="A" /> <genomic_allele id="8" sequence="G" /> </genomic_polymorphism> <panel id="101" lsid="urn:lsid:ims.u-tokyo.ac.jp:JSNP:JBIC" ethnicity="Japanese" count_unit="chromosome" size="1504"> <annotation name="description" value="752 unrelated Japanese volunteers" /> </panel> <polymorphism_assay id="102" description="Amplification of samples by multiplex PCR and by Invader assay combines structure-specific cleavage enzymes and a universal fluorescent resonance energy transfer (FRET) system with the 384-well reaction card"> <db_xref db="JSNP" uid="m2" url="http://snp.ims.u-tokyo.ac.jp/JBICSamplesMethods.html" /> <molecular_sample> <panel id="101"> <genomic_allele_population_frequency value="0.4328" > <source db="JSNP" /> <db_xref db="JSNP" uid="IMS-JST070162" url="http://snp.ims.u-tokyo.ac.jp/cgi-bin/SnpInfo.cgi?SNP_ID=IMS-JST070162" /> <panel id="101"/> <genomic_allele id="7"/> <contributor name="JBIC" /> </genomic_allele_population_frequency> <genomic_allele_population_frequency value="0.5672" > <source db="JSNP" /> <panel id="101"/> <genomic_allele id="8"/> </genomic_allele_population_frequency> </panel> </molecular_sample> </polymorphism_assay> <genomic_gene_structure id="10" gene_symbol="CA6"> <exon> <reference_genomic_location start="3543307" end="3543391" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </exon> <exon> <reference_genomic_location start="3546689" end="3546868" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </exon> <exon> <reference_genomic_location start="3554563" end="3554711" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </exon> <exon> <reference_genomic_location start="3556336" end="3556428" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </exon> <exon> <reference_genomic_location start="3560013" end="3560082" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </exon> <exon> <reference_genomic_location start="3565085" end="3565242" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </exon> <exon> <reference_genomic_location start="3568293" end="3568407" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </exon> <exon> <reference_genomic_location start="3572048" end="3572513" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </exon> <cds> <reference_genomic_location start="3543313" end="3572130" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NT_021937.17" field="version" /> </reference_genomic_landmark> </reference_genomic_location> </cds> </genomic_gene_structure> <genic_polymorphism id="11" label="point" original_residue="A" changed_residue="G"> <reference_genomic_location start="274" end="274" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NM_001215.1" field="version" /> </reference_genomic_landmark> </reference_genomic_location> <genomic_polymorphism id="9" /> <genomic_gene_structure id="10" gene_symbol="CA6"> <exon /> </genomic_gene_structure> <transcription_change id="12" /> </genic_polymorphism> <transcription_change id="12" label="truncation" codon_position="1" original_residue="A" changed_residue="G" original_codon="AGC" changed_codon="GGC"> <genic_polymorphism id="11" /> <translation_change id="13" /> </transcription_change> <translation_change id="13" label="nonsynonymous" original_residue="S" changed_residue="G"> <reference_genomic_location start="90" end="90" strand="1"> <reference_genomic_landmark> <db_xref db="RefSeq" uid="NP_001206.1" field="version" /> </reference_genomic_landmark> </reference_genomic_location> <transcription_change id="12" /> </translation_change> </pml>