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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs9923231          **clinically associated**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:link to VariationViewerlink to OMIM
HGVS Names
NT_010393.15:g.22420768C>T
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss13761958 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9923231 during BLAST analysis for the current build.

NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss13761958BCM_SSAHASNP|chr16.NT_024812.10_2507356fwd/BC/Tgctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt11/05/0311/22/03119Genomicunknown
ss21316156SSAHASNP|WGSA-200403-chr16.chr16.NT_024812.10_2507356fwd/BC/Tgctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt03/19/0403/19/04121Genomicunknown
ss28527760PGA-UW-FHCRC|VKORC1-003673byFreqrev/TA/Gaagagaagacctgaaaaacaaccattggccggtgcggtggctcacgcctataatcctagc11/06/0401/27/05126Genomicunknown
ss75181539ILLUMINA|ILMN_Human_1M_rs9923231fwd/BC/Tgctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt08/28/0708/29/07129Genomicunknown
ss77595664HGSV|Cor12156_SNV_20070510.chr16_31015190fwd/BC/Tgctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt10/09/0710/13/07129Genomicunknown
ss83709285HGSV|Cor18956_SNV_20070510.chr16_31015190fwd/BC/Tgctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt11/30/0712/05/07130Genomicunknown
ss90365531BCMHGSC_JDW|JWB-0937825fwd/BC/Tgctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt02/26/0802/29/08129Genomicunknown
ss103290726BGI|BGI_rs9923231fwd/BC/Tgctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt06/06/0806/18/09130Genomicunknown
ss105108094PHARMGKB_PEAR|PS206819_PA152215506_141fwd/TA/Ggctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt07/23/0807/23/08130Genomicunknown
ss105109748PHARMGKB_PEAR|PS207473_PA155617125_141fwd/TA/Ggctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt07/23/0807/23/08130Genomicunknown
ss1092986301000GENOMES|CEU.trio.12.15.2008_3282525_chr16_31015190fwd/BC/Tgctaggattataggcgtgagccaccgcaccggccaatggttgtttttcaggtcttctctt12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9923231|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TAAGAGGTCC TTCACCAGCC TCCTCTCCCG GCATTATCCC ATCTACCCCT CCACATTCAA
 GTTTTTGGAA AGATTCTACA CTCCCAGTCT CTACTTCCTC ACTTCTTCCT TGCTGCCCAC
 GCCATAAACT AGCTGCTGCC TCCAGCATTG CCCTGACACC TAGTGGCTGG TGTCACCAAG
 ACGCTAGACC CAATGGttat ttatttattt atttacttat tttgagacgg agtctcactc
 tgtcgcccag gctggagtgc agcggtgcca tctcggctca ctgcaacttc cgcctccagg
 gttcaagtgg ttctcgtgcc tcagcctccc aagtagtttg gactacaggt gcctgccacc
 atgtctggct aatttttgta tttttagtag agacagggtt tcaccatgtt ggccaggctt
 gtcttaaact cctgacctca agtgatccac ccacctcggc ctcccaaaat gctaggatta
 taggcgtgag ccaccgcacc
 Y
 ggccAATGGT TGTTTTTCAG GTCTTCTCTT GCTTGACTTC CCAGAGGGAT CCCTTACTGT
 TGCACCTACC CTTCTGGGAA CTCTCTTCCT CTGGCGTCTG TGATATTTCC CTCTCCTGCT
 GGCTCCTCCC TCTCCAGATG CTGTTTCTCA CATCTACTCT CTTCTAGAGA Gtgtggtaga
 cagaataatg gtcaccaaag atgtccctgc atgaatccct ggaacttgtg aatatgatag
 gttaaatggc caaaagggaa ttaaggttgc agatggaatt aagctgacca atctCCTGat
 tttattttat tttattttgt ttttgaggtg gagtttcgct cttgttgccc aactggagtg
 caatggtgtg atctcggctc actgcaacct ccgcctgcca ggttcgagag attctcctgc
 ctcagcctcc cgagtagctg ggattacagg cacccgccat catgcctggc taatttttta
 aatttttagt agagacaggg

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_024812
dbSNP Blast Analysis
OMIM
608547.0006

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP A
 C
 G
 T
ss105108094 PA152215507 694 AF 0.347 0.653
ss105109748 PA155617126 410 AF 0.500 0.500
ss28527760 PGA-AFRICAN-PANEL African American 40 IG 0.750 0.250 0.527 0.875 0.125
PGA-EUROPEAN-PANEL European 44 IG 0.318 0.500 0.182 1.000 0.568 0.432

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.408+/-0.194 1239 1028 15 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN YES

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Revised: May 25, 2006 1:38 PM .