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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2239710          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NG_000018.2:g.53329T>C
NM_021013.3:c.839T>C
NP_066293.2:p.Ile280Thr
NT_010755.15:g.3260155A>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 ss40855720 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2239710 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
ss3195027YUSUKE|IMS-JST010945byFreqfwd/BC/Tccaggagtcagtatgaggctctggtggaaataaccgcagggaagtggagcaatggttcgc08/07/0110/10/0398Genomicunknown
ss6756951WI_SSAHASNP|NT_024901.11_1058647rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg02/12/0310/25/06111Genomicunknown
ss14302555BCM_SSAHASNP|chr17.NT_010755.14_3258357rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg11/05/0311/22/03119Genomicunknown
ss15764952SC_SNP|NT_010755.14_3258357rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg11/17/0311/22/03120Genomicunknown
ss21429998SSAHASNP|WGSA-200403-chr17.chr17.NT_010755.14_3258357rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg03/19/0403/20/04121Genomicunknown
ss24117955PERLEGEN|afd0819531byFreqrev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg08/10/0409/13/04124Genomicunknown
ss28498683MGC_GENOME_DIFF|37543812-A3258357Grev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg08/20/0408/20/04126cDNAunknown
ss28513625MGC_GENOME_DIFF|BC041070x37543812-A3258357Grev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg08/25/0408/25/04126cDNAunknown
ss40855720ABI|hCV2554390byFreqrev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg07/17/0511/03/06126Genomicunknown
ss48407736APPLERA_GI|hCV2554390byFreqrev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg09/28/0511/03/06126Genomicunknown
ss66806308ILLUMINA|HumanHap300v1.1_rs2239710fwd/TC/Tccaggagtcagtatgaggctctggtggaaataaccgcagggaagtggagcaatggttcgc11/09/0611/09/06127Genomicunknown
ss67236586ILLUMINA|HumanHap550v1.1_rs2239710fwd/BC/Tccaggagtcagtatgaggctctggtggaaataaccgcagggaagtggagcaatggttcgc11/14/0611/14/06127Genomicunknown
ss67632804ILLUMINA|HumanHap650Yv1.0_rs2239710fwd/BC/Tccaggagtcagtatgaggctctggtggaaataaccgcagggaagtggagcaatggttcgc11/14/0611/14/06127Genomicunknown
ss70714913ILLUMINA|HumanHap550v3.0__rs2239710rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg04/20/0703/30/08130Genomicunknown
ss71282714ILLUMINA|HumanHap650Yv3.0_rs2239710fwd/BC/Tccaggagtcagtatgaggctctggtggaaataaccgcagggaagtggagcaatggttcgc04/23/0704/23/07127Genomicunknown
ss75849144ILLUMINA|ILMN_Human_1M_rs2239710fwd/BC/Tccaggagtcagtatgaggctctggtggaaataaccgcagggaagtggagcaatggttcgc08/28/0708/29/07129Genomicunknown
ss79122454ILLUMINA|HumanHap300v2.0_rs2239710fwd/BC/Tccaggagtcagtatgaggctctggtggaaataaccgcagggaagtggagcaatggttcgc04/18/0711/18/07130Genomicunknown
ss84005038KRIBB_YJKIM|KHS599175fwd/BC/Tccaggagtcagtatgaggctctggtggaaataaccgcagggaagtggagcaatggttcgc12/04/0712/06/07130Genomicunknown
ss85722721HGSV|Cor19129_SNV_20070510.chr17_36789385rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg12/06/0712/10/07130Genomicunknown
ss85905538HGSV|Cor18517_SNV_20070510.chr17_36789385rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg12/06/0712/10/07130Genomicunknown
ss85914357HGSV|Cor18956_SNV_20070510.chr17_36789385rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg11/30/0712/10/07130Genomicunknown
ss90587473BCMHGSC_JDW|JWB-1021123rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg02/26/0802/29/08129Genomicunknown
ss96545673HUMANGENOME_JCVI|1103645324316rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg03/26/0803/26/08130Genomicunknown
ss1097622581000GENOMES|CEU.trio.12.15.2008_3398319_chr17_36789385rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg12/15/0812/16/08130Genomicunknown
ss1135302871000GENOMES|NA19240_2008_12_16_3057549_chr17_36789385rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg12/18/0812/18/08130Genomicunknown
ss118053745ILLUMINA-UK|NA18507_000042932_NCBI36.1_chr17_36789385rev/TA/Ggcgaaccattgctccacttccctgcggttatttccaccagagcctcatactgactcctgg01/20/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2239710|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CAGCAATTGA TGTGATCCCT GTTGGAGTTT ATTGCTATAA AATGTGTGTG TCACTCTTTG
 GGAATGATCA GAATATTCCT TTTAGTGCTT TTTGGGCAGT ATTGTGCTCA TTTCCCTGGA
 GCAGGAAAAT GGCAGATCCA TTGCCGTAGG TTCATTGTTT CCCTTTTCTC CAACAGGAGG
 TTAACACCCT GCGCTCCCAG CTTGGAGACC GCCTCAACGT GGAGGTGGAC ACTGCCCCCA
 CTGTGGACCT GAACCAGGTC CTGAACGAGA CCAGGAGTCA GTATGAGGCT CTGGTGGAAA
 Y
 TAACCGCAGG GAAGTGGAGC AATGGTTCGC CACGCAGGTG GGCATCTAAG CACATGGCCA
 CTCAGGACCC GAGGTGCCCC AGGGCCCTGG AGACAGGGTC TGATCCTTTC CCCACTTGGG
 TGTTTCAGAC CGAGGAGCTG AACAAGCAGG TGGTATCCAG CTCAGAGCAG CTGCAGTCCT
 GCCAGGCGGA GATCATCGAG CTGAGACGCA CAGTCAACGC CCTGGAGATC GAGCTGCAGG
 CCCAGCACAA CCTGGTGTGT ATTGTTCAGA CCTGCTGGTG AGCGATGGGA ACTTGGGAGG

  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
Y16790.1 ABBA01031811 BC041070
dbSNP Blast Analysis
UniGene Cluster ID
296942

  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
ss24117955 AFD_EUR_PANEL European 46 IG 0.391 0.522 0.087 0.479 0.652 0.348
AFD_AFR_PANEL African American 46 IG 0.957 0.043 1.000 0.978 0.022
AFD_CHN_PANEL Asian 48 IG 0.375 0.500 0.125 0.752 0.625 0.375
ss3195027 JBIC-allele 1452 AF 0.585 0.415
ss40855720 HapMap-CEU European 120 IG 0.267 0.583 0.150 0.200 0.558 0.442
HapMap-HCB Asian 88 IG 0.409 0.455 0.136 1.000 0.636 0.364
HapMap-JPT Asian 88 IG 0.341 0.432 0.227 0.439 0.557 0.443
HapMap-YRI Sub-Saharan African 120 IG 0.967 0.033 1.000 0.983 0.017
ss48407736 AGI_ASP population multiple 76 IG 0.658 0.237 0.105 0.050 0.776 0.224

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict		 Additional Freq. Data
0.405+/-0.196 1303 1091 15 0 ALFRED: The Allele Frequency Database

  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: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .