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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs9625679          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_015370.1:c.136T>C
NP_056185.1:p.Cys46Arg
NT_011520.11:g.8847268A>G
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 ss76891140 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9625679 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
ss13390689SC_SNP|NT_011520.9_8847268fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc10/23/0310/31/03119Genomicunknown
ss19494584CSHL-HAPMAP|CSHL-HuDD-200402.chr22.NT_011520.9_8847268fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc02/20/0403/04/04120Genomicunknown
ss44303278ABI|hCV2479944byFreqfwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc07/18/0511/03/06126Genomicunknown
ss48404145APPLERA_GI|hCV2479944fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc09/28/0511/30/05126Genomicunknown
ss65730141ILLUMINA|Human1-rs9625679fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc10/10/0610/10/06127Genomicunknown
ss66568340ILLUMINA|HumanHap300v1.1_rs9625679fwd/BA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc11/09/0611/09/06127Genomicunknown
ss67937395ILLUMINA|HumanHap550v1.1_rs9625679fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc11/14/0611/15/06127Genomicunknown
ss68054825ILLUMINA|HumanHap650Yv1.0_rs9625679fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc11/14/0611/15/06127Genomicunknown
ss69274751PERLEGEN|PGP00119554byFreqfwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc01/30/0703/31/08127Genomicunknown
ss71619560ILLUMINA|HumanHap650Yv3.0_rs9625679fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc04/23/0704/23/07127Genomicunknown
ss74809723AFFY|SNP_M-182715fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc08/09/0708/09/07128Genomicunknown
ss75808599ILLUMINA|ILMN_Human_1M_rs9625679fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc08/28/0708/29/07129Genomicunknown
ss76891140SI_EXO|NT_011520.11_8847268fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc09/20/0709/20/07129Genomicunknown
ss79301694ILLUMINA|HumanHap300v2.0_rs9625679fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc04/18/0711/18/07130Genomicunknown
ss84845156KRIBB_YJKIM|KHS827466fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc12/04/0712/08/07130Genomicunknown
ss98279084ILLUMINA|HumanHap550v3.0__rs9625679fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc04/20/0703/31/08130Genomicunknown
ss1141247471000GENOMES|NA19240_2008_12_16_3433039_chr22_27786699fwd/TA/Ggtgctggggcattaatgttctgctttgcactgttctggccatccagatgttggtgagagc12/18/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9625679|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GCGGTAGCCG CACGCCATAT AATCTCAACC GTTAAGTGTT CTCTGGCTTT ACCTTTTCCC
 TCCCCTCGCC AGTCACATTT TCCCCACCAC TGGTCCTCGT CTACCTCTCT GATGCCTCCT
 GCAGGCCTCC TATGCCCTGC TGGCTGCTTG CTCTTGGAAC TGATGAAGTT TCTTTTCCTG
 GCCTGCTGGG TGGCTTTCAT CACTGAATCG TCCTTGTGCT TTAATCTCTT CGAGAGTTTT
 CCTTCTCCAA ACTTGCATGG TGGTGGGCAG CACTTATTCT TCAGTTGCCG CCTGAGTACA
 AGCTTAACCA GGGAGAAGGA ACTGGCAATT AATGGGTTCC TTACAACTTC CCAAGAGGAA
 GTGGTAGCTG GTGCTGGGGC ATTAATGTTC TGCTTTGCAC
 R
 TGTTCTGGCC ATCCAGATGT TGGTGAGAGC CGGTGAGTCC ACATAGCAGT CCTGAAGCCT
 GGTATTTAAT AAGATGGACT GTCGGAGTCC ATAGATAGGG ATGCTGGGGT CTCGTCTCAC
 ATTGATTGGG TGCTAGAATT ATAAGGAGGG AGAAATGAAT TTTAAAAGGA CCGTTCTTCA
 GCAGAGAATA AAAGGTCTAC TTTGAAGGCA AAATATTAAC ATCTTTTTAT AGGCCATTCC
 TTCCACCCAG TTCTTAGAAA TTTACTATAT GTCCTCTCCT GTTCACCAAA GCCTTTTATA
 CCAAGTAGGG AGGAGATAGT CACTCCACAA GGTTACAGTA ATATTCAGGC TCTCAAAGAA
 CATAGCATGC CAGGGCAGGA AGTCGGGGGT CAGGGAGGGT

  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_011520.11
dbSNP Blast Analysis
UniGene Cluster ID
50891

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss44303278 HapMap-CEU European 120 IG 0.933 0.067 1.000 0.967 0.033
HapMap-HCB Asian 90 IG 0.644 0.333 0.022 0.584 0.811 0.189
HapMap-JPT Asian 88 IG 0.568 0.341 0.091 0.439 0.739 0.261
HapMap-YRI Sub-Saharan African 120 IG 0.617 0.350 0.033 0.655 0.792 0.208
ss48404145 AGI_ASP population multiple 52 IG 0.962 0.038 1.000 0.981 0.019
ss69274751 HapMap-CEU European 120 GF 0.933 0.067 0.967 0.033
HapMap-HCB Asian 90 GF 0.644 0.333 0.022 0.811 0.189
HapMap-JPT Asian 90 GF 0.556 0.356 0.089 0.733 0.267
HapMap-YRI Sub-Saharan African 120 GF 0.617 0.350 0.033 0.792 0.208

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.265+/-0.250 1239 1034 270 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 UNKNOWN

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Revised: May 25, 2006 1:38 PM .