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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2287949          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_001012509.1:c.987G>A
NM_016180.3:c.987G>A
NT_006576.15:g.33927268T>C
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 ss48428069 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2287949 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
ss3228925YUSUKE|IMS-JST039009byFreqfwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg09/05/0110/10/03100Genomicunknown
ss10242246BCM_SSAHASNP|chr5.NT_006576.13_16380704fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg06/27/0310/10/03116Genomicunknown
ss14840653SC_SNP|NT_006576.14_16406617fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg11/12/0311/22/03119Genomicunknown
ss17061415CSHL-HAPMAP|CSHL-HuAA-200402.chr5.NT_006576.14_16406617fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg02/17/0403/04/04120Genomicunknown
ss17837714CSHL-HAPMAP|CSHL-HuCC-200402.chr5.NT_006576.14_16406617fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg02/19/0403/04/04120Genomicunknown
ss22300728SSAHASNP|WGSA-200403-chr5.chr5.NT_006576.14_16406617fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg03/21/0403/21/04121Genomicunknown
ss23456969PERLEGEN|afd4653623byFreqfwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg08/10/0409/13/04123Genomicunknown
ss28509542MGC_GENOME_DIFF|BC064405x37550355-T16406617Cfwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg08/25/0408/25/04126cDNAunknown
ss48428069APPLERA_GI|hCV16183421byFreqfwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg09/28/0511/03/06126Genomicunknown
ss65741671ILLUMINA|Human1-rs2287949fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg10/10/0610/10/06127Genomicunknown
ss74910232ILLUMINA|ILMN_Human_1M_rs2287949fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg08/28/0708/29/07129Genomicunknown
ss77212609HGSV|Cor12156_SNV_20070510.chr5_33990268fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg10/09/0710/11/07129Genomicunknown
ss78106599HGSV|Cor12878_SNV_20070510.chr5_33990268fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg10/17/0710/17/07129Genomicunknown
ss81243880HGSV|Cor18507_SNV_20070510.chr5_33990268fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg11/26/0711/28/07130Genomicunknown
ss82091009HGSV|Cor18956_SNV_20070510.chr5_33990268fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg11/30/0712/02/07130Genomicunknown
ss82240922HGSV|Cor19240_SNV_20070510.chr5_33990268fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg11/30/0712/02/07130Genomicunknown
ss93054670BCMHGSC_JDW|JWB-1961150fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg02/26/0803/03/08129Genomicunknown
ss98610236HUMANGENOME_JCVI|1103654071259fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg04/01/0804/01/08130Genomicunknown
ss1089477691000GENOMES|CEU.trio.12.15.2008_1241472_chr5_33990268fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg12/15/0812/16/08130Genomicunknown
ss1116721911000GENOMES|NA19240_2008_12_16_1112113_chr5_33990268fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg12/16/0812/17/08130Genomicunknown
ss116560613ILLUMINA-UK|NA18507_000052180_NCBI36.1_chr5_33990268fwd/BC/Ttgtgaagaacagcatgttggacaggaaggcgtccatccaatgaggtggctgatgcaaagg01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2287949|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TAATGGGAGA CTTTAACACC CCACTGTCAA CTATTTGTTG TATTTGATTA AATACTGGCA
 GGCTCCGTAG TGTCCTCTAG TTGTCCAGGG TATAGTAGCA TTTTTCTACA CCTGTCTGTA
 AGTCAGCTTC TTGATGGTAC CCTTTCCTAC ATTCTTACTG TGCCAATCTT AGAGGATAGC
 CCAGAAGAAC CTCAACAGGT GTTAATGGAG GAAATGATGT GTAACAGTGA TTGTGTGCAC
 AGACACGTTC ATTACCTGGC CCATGAAATC TGTGAAGAAC AGCATGTTGG ACAGGAAGGC
 Y
 GTCCATCCAA TGAGGTGGCT GATGCAAAGG TAGCGGTAGT GAGGAGGCAT GTTCACCAGT
 GCTCTCAGCA GTGACTTTAA TGTCATTGCC CTGCGAGTCT GAAATAAAAC ATGAAACAGA
 GGTGTGATCT TCACTGCAGA AACTCAGCCA GCTAAGGGAG CCAGAACACA CAGACATGTT
 ATGTATTTGT CAGTCAGCCA TCACACAAAG TGTCACTTTT CCTGGACATG GAACTAGGTT
 TCCATGGAGT AGACTCACAG GAGGTATTCT GTTAAGCACG AGTGGCTGCT TGGCAGTTTC

  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_006576 ABBA01066761 BC064405
dbSNP Blast Analysis
UniGene Cluster ID
278962

  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
ss23456969 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.739 0.217 0.043 0.479 0.848 0.152
AFD_CHN_PANEL Asian 48 IG 0.708 0.292 0.439 0.854 0.146
ss3228925 JBIC-allele 1498 AF 0.734 0.266
ss48428069 HapMap-CEU European 118 IG 1.000 1.000
HapMap-HCB Asian 82 IG 0.732 0.220 0.049 0.273 0.841 0.159
HapMap-JPT Asian 90 IG 0.556 0.444 0.100 0.778 0.222
HapMap-YRI Sub-Saharan African 116 IG 0.759 0.241 0.317 0.879 0.121
AGI_ASP population multiple 66 IG 0.939 0.061 1.000 0.970 0.030

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict		 Additional Freq. Data
0.184+/-0.241 1300 1088 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
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .