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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2981430          
refSNP ID: rs2981430
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:101/129
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_000141.3:c.455-725C>T
NM_022970.2:c.455-725C>T
NT_030059.12:g.42060224G>A
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 ss20705234 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2981430 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
ss4195819SC_JCM|AF360695.3_19176fwd/BC/Tatcacttgtatttatgactttcggggacattggagggcataactttaacatatcatttaa10/15/0105/28/04101Genomicunknown
ss4383871COX|FGFR2-44813fwd/BC/Tatcacttgtatttatgactttcggggacattggagggcataactttaacatatcatttaa02/28/0210/10/03103Genomicunknown
ss6073171SC_JCM|NT_030764.5_559468rev/TA/Gttaaatgatatgttaaagttatgccctccaatgtccccgaaagtcataaatacaagtgat01/10/0310/10/03111Genomicunknown
ss15786078SC_SNP|NT_030059.11_42060224rev/TA/Gttaaatgatatgttaaagttatgccctccaatgtccccgaaagtcataaatacaagtgat11/17/0311/22/03120Genomicunknown
ss20705234SSAHASNP|WGSA-200403-chr10.chr10.NT_030059.11_42060224byFreqrev/TA/Gttaaatgatatgttaaagttatgccctccaatgtccccgaaagtcataaatacaagtgat03/18/0405/17/04121Genomicunknown
ss24103137PERLEGEN|afd2312056byFreqrev/TA/Gttaaatgatatgttaaagttatgccctccaatgtccccgaaagtcataaatacaagtgat08/10/0409/13/04123Genomicunknown
ss52973993EGP_SNPS|FGFR2-048155byFreqfwd/BC/Tatcacttgtatttatgactttcggggacattggagggcataactttaacatatcatttaa06/05/0612/16/06127Genomicunknown
ss67689670ILLUMINA|HumanHap650Yv1.0_rs2981430fwd/BC/Tatcacttgtatttatgactttcggggacattggagggcataactttaacatatcatttaa11/14/0611/14/06127Genomicunknown
ss69093868PERLEGEN|PGP02312056byFreqrev/TA/Gttaaatgatatgttaaagttatgccctccaatgtccccgaaagtcataaatacaagtgat01/30/0703/31/08127Genomicunknown
ss71339772ILLUMINA|HumanHap650Yv3.0_rs2981430fwd/BC/Tatcacttgtatttatgactttcggggacattggagggcataactttaacatatcatttaa04/23/0704/23/07127Genomicunknown
ss74838166AFFY|SNP_M-596158fwd/BC/Tatcacttgtatttatgactttcggggacattggagggcataactttaacatatcatttaa08/09/0708/09/07128Genomicunknown
ss75353775ILLUMINA|ILMN_Human_1M_rs2981430fwd/BC/Tatcacttgtatttatgactttcggggacattggagggcataactttaacatatcatttaa08/28/0708/29/07129Genomicunknown
ss80746040KRIBB_YJKIM|KHS1008173fwd/BC/Tatcacttgtatttatgactttcggggacattggagggcataactttaacatatcatttaa11/26/0711/26/07130Genomicunknown
ss82256593HGSV|Cor18956_SNV_20070510.chr10_123301688rev/TA/Gttaaatgatatgttaaagttatgccctccaatgtccccgaaagtcataaatacaagtgat11/30/0712/02/07130Genomicunknown
ss82422701HGSV|Cor19240_SNV_20070510.chr10_123301688rev/TA/Gttaaatgatatgttaaagttatgccctccaatgtccccgaaagtcataaatacaagtgat11/30/0712/02/07130Genomicunknown
ss88384306BCMHGSC_JDW|JWB-0346438rev/TA/Gttaaatgatatgttaaagttatgccctccaatgtccccgaaagtcataaatacaagtgat02/26/0802/27/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2981430|allelePos=442|totalLen=665|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 ACGGATTCCA ACCTCGTGGA GAAGCTGCAT CTTCTTAGca gtggagagta gggttgaaga
 tagtgggctc tggcatcaga ctgatgtggt tcaaatcttg gctgcacctc ttccaagctt
 tgtggctttt ggcaggttac ttaactgctc tgtgcctcag tttccccact tggaagccaa
 gattatgata gtgcctttct tgttgaagca ttgtgaagat taatgtgttg acatgtaaaa
 actctttgag cagtgcttgg caaagtagaa gctttcagtC GGTAGTAGTC ATTCGCCATT
 ATTAGCAGAC ATGAAGAATT TACAGTGGTA TTCTGGCTTG ATGTTGTGGC TTTTATTTAG
 AAAAAATATA CTTTACTTTG TGATTTAAAA CTTTTTTCTT GACTTTAAAA AATCACTTGT
 ATTTATGACT TTCGGGGACA T
 Y
 TGGAGGGCAT AACTTTAACA TATCATTTAA TTGGTAGCCT CCTCTTAAGT TATCATTAGG
 TGGGGTGGTA GGGTTATGGC ATTCATAACC ACCATTGGAA AGaaattttt tttttaatta
 aaaaaGTTAG TATGTATTTA GTGATACAGT TTTTTTTTTT GTTTGTTTGT TTGTATATAA
 GTTCTGAGAA ATGTACGAAT GACTCTCTGG GTTATTTTAT TAT

  GeneView back to top
GeneView via analysis of contig annotation: FGFR2 fibroblast growth factor receptor 2
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_030059->NM_000141
function
referenceNT_030059->NM_022970
function
HuRefNW_001838006->NM_000141
function
HuRefNW_001838006->NM_022970
function
CeleraNW_924884->NM_000141
function
CeleraNW_924884->NM_022970
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_030059->NM_000141->NP_00013242060224reverseintron
referenceNT_030059->NM_022970->NP_07525942060224reverseintron
HuRefNW_001838006->NM_000141->NP_0001321689061forwardintron
HuRefNW_001838006->NM_022970->NP_0752591689061forwardintron
CeleraNW_924884->NM_000141->NP_00013234046724reverseintron
CeleraNW_924884->NM_022970->NP_07525934046724reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2981430 maps exactly once on NCBI human chromosome 10
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
10NW_001838006.21689061116942623plusTalt_assembly_8HuRefHuRefview441
10NW_924884.134046724117043907minusAalt_assembly_1CeleraCeleraview441
10NT_030059.1242060224123301688minusGref_assemblyreferencereferenceview441

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_030764.5 AC009988
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
N
T
ss20705234CHMJAsian 74IG 0.554 0.162 0.284
ss24103137AFD_EUR_PANELEuropean 46IG 0.217 0.348 0.435 0.200 0.391 0.609
AFD_AFR_PANELAfrican American 44IG 0.045 0.364 0.591 1.000 0.227 0.773
AFD_CHN_PANELAsian 48IG 0.250 0.583 0.167 0.403 0.542 0.458
ss52973993EGP_YORUB-PANELSub-Saharan African 24IG 0.083 0.167 0.750 0.200 0.167 0.833
EGP_HISP-PANELHispanic 44IG 0.182 0.455 0.364 1.000 0.409 0.591
EGP_CEPH-PANELEuropean 44IG 0.182 0.591 0.227 0.403 0.477 0.523
EGP_AD-PANELAfrican American 30IG 0.067 0.467 0.467 0.752 0.300 0.700
EGP_ASIAN-PANELAsian 48IG 0.208 0.667 0.125 0.100 0.542 0.458
ss69093868HapMap-CEUEuropean 120GF 0.133 0.533 0.333 0.400 0.600
HapMap-HCBAsian 90GF 0.222 0.511 0.267 0.478 0.522
HapMap-JPTAsian 90GF 0.333 0.622 0.044 0.644 0.356
HapMap-YRISub-Saharan African 120GF 0.067 0.300 0.633 0.217 0.783

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.484+/-0.088355283810

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hit
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNYES

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Revised: May 25, 2006 1:38 PM .