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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs924397          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NT_025741.14:g.23902465C>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 ss44773530 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs924397 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
ss1361631TSC-CSHL|TSC0239700byFreqfwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct09/06/0004/07/0486Genomic95 %
ss12911572SC_SNP|NT_025741.12_23902465fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct10/21/0310/31/03119Genomicunknown
ss15741870SC_SNP|NT_025741.13_23902465fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct11/17/0311/22/03120Genomicunknown
ss44773530ABI|hCV8274786byFreqfwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct07/19/0511/03/06126Genomicunknown
ss66629541ILLUMINA|HumanHap300v1.1_rs924397fwd/TC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct11/09/0611/09/06127Genomicunknown
ss67896258ILLUMINA|HumanHap550v1.1_rs924397fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct11/14/0611/14/06127Genomicunknown
ss68030522ILLUMINA|HumanHap650Yv1.0_rs924397fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct11/14/0611/15/06127Genomicunknown
ss71595171ILLUMINA|HumanHap650Yv3.0_rs924397fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct04/23/0704/23/07127Genomicunknown
ss75476620ILLUMINA|ILMN_Human_1M_rs924397fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct08/28/0708/29/07129Genomicunknown
ss79289943ILLUMINA|HumanHap300v2.0_rs924397fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct04/18/0711/18/07130Genomicunknown
ss83614350KRIBB_YJKIM|KHS502089fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct12/04/0712/05/07130Genomicunknown
ss98237712ILLUMINA|HumanHap550v3.0__rs924397rev/TA/Gagcctgtctgtatctctctccttcatgcgctaatcctcattctgccctttataaataata04/20/0703/31/08130Genomicunknown
ss1108140281000GENOMES|CEU.trio.12.15.2008_1610044_chr6_119839729fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct12/15/0812/17/08130Genomicunknown
ss116691358ILLUMINA-UK|NA18507_000162050_NCBI36.1_chr6_119839729fwd/BC/Ttattatttataaagggcagaatgaggattagcgcatgaaggagagagatacagacaggct01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs924397|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 AAACAAGAAA AATAAATATA TCGCCCCAAT TCACTGGAGG AGTCTGGAAT TGAGCAAAAT
 TAAAACAATT TCTCTGTAGC CAGCACCACA GCAGGAGCTG GGCTCTCTGA CACATGTGAA
 ACACTCTTTC TGTGTGTAAA TATTTTTAAA TTGCCTTGTT AAAGAAAAGA GGAAACCCAG
 GCAGAGTCAT ACATTGCCCA GATGTATCGG ATCAGAAGAA TGAAAGTGCA AAAGGTCAGA
 GACTCTATTC TGAAGAGGAG AGAATATCTC TATTATTTAT AAAGGGCAGA ATGAGGATTA
 Y
 GCGCATGAAG GAGAGAGATA CAGACAGGCT GCCCCTGGAA AATTAATGGA GCACTGGAAG
 GTGCAAGCAG AAAAAAATCC TGGCCACCTG TGAATTGGGT TAGAGAAAAG AGGAAAGGCT
 TTTGTACAGA TATCCTGCAA TATGAGGGCT AAAGGTCTCC CTACAAGTAG GTGATTGCTT
 ATTGATCCTA ATTTCCCCTA TGTACACTAC TGAGGAACAC CAAGAAGAAA AGTTCTTCCA
 ACAAAAACAA CGTTTTGATG TCTGTCCCTC ACTCAATTTT AAAAATTTTC AAGGTGGACT

  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_025741
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss1361631 TSC_42_AA 78 AF 0.526 0.474
TSC_42_C 82 AF 0.744 0.256
TSC_42_A 78 AF 0.526 0.474
ss44773530 HapMap-CEU European 120 IG 0.600 0.367 0.033 0.584 0.783 0.217
HapMap-HCB Asian 90 IG 0.356 0.444 0.200 0.584 0.578 0.422
HapMap-JPT Asian 88 IG 0.295 0.523 0.182 0.752 0.557 0.443
HapMap-YRI Sub-Saharan African 120 IG 0.217 0.483 0.300 1.000 0.458 0.542

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.481+/-0.096 1207 1002 0 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: ILLUMINA
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .