NCBI

NLM

PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
Spacer gif
BUILD 129
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs2239641          
refSNP ID: rs2239641
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/129
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_003234.1:c.1468+39A>G
NT_029928.12:g.409148T>C
Links

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 ss10060574 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2239641 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
ss3194930YUSUKE|IMS-JST010848fwd/TA/Gccctttcattagctgtgtatgaattcaggtaacttttttgagatggagttttgctcttgt08/07/0110/10/0398Genomicunknown
ss10060574BCM_SSAHASNP|chr3.NT_029928.10_409148rev/BC/Tacaagagcaaaactccatctcaaaaaagttacctgaattcatacacagctaatgaaaggg06/27/0310/10/03116Genomicunknown
ss14229702BCM_SSAHASNP|chr3.NT_029928.11_409148rev/BC/Tacaagagcaaaactccatctcaaaaaagttacctgaattcatacacagctaatgaaaggg11/05/0311/22/03119Genomicunknown
ss21968527SSAHASNP|WGSA-200403-chr3.chr3.NT_029928.11_409148rev/BC/Tacaagagcaaaactccatctcaaaaaagttacctgaattcatacacagctaatgaaaggg03/20/0403/20/04121Genomicunknown
ss24608620PERLEGEN|afd0794318byFreqrev/BC/Tacaagagcaaaactccatctcaaaaaagttacctgaattcatacacagctaatgaaaggg08/10/0409/13/04123Genomicunknown
ss52974650RSG_UW|TFRC-021539byFreqfwd/TA/Gccctttcattagctgtttatgaattcaggtaacttttttgagatggagttttgctcttgt06/06/0612/16/06127Genomicunknown
ss81140647HGSV|Cor18555_SNV_20070510.chr3_197277724rev/BC/Tacaagagcaaaactccatctcaaaaaagttacctgaattcatacacagctaatgaaaggg11/27/0711/28/07130Genomicunknown
ss81189323HGSV|Cor18507_SNV_20070510.chr3_197277724rev/BC/Tacaagagcaaaactccatctcaaaaaagttacctgaattcatacacagctaatgaaaggg11/26/0711/28/07130Genomicunknown
ss92429829BCMHGSC_JDW|JWB-1721968rev/BC/Tacaagagcaaaactccatctcaaaaaagttacctgaattcatacacagctaatgaaaggg02/26/0803/03/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2239641|allelePos=201|totalLen=1344|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GTCTCAGTAG AGTCCAGAAT TGAAAATGAA TCCCTAATGC TACTGTATGT GATAAATAAA
 CAGATTTATA CTTATTAGTG TTTTCCCTTC TCTTCTAGGG ATACCTTTCG TCCCTGCATT
 TAAAGGCTTT CACTTATATT AATCTGGATA AAGCGGTTCT TGGTAAGTAT CCCTTTCATT
 AGCTGTGTAT GAATTCAGGT
 R
 AACttttttg agatggagtt ttgctcttgt cgcccaggct ggagtgcaat ggcacgatct
 cggctcactg caacctctgt ctcccagatt caagcgattc tcctgcctta gcctcctgag
 tagctgggat tacaggtgct cactaccaca cccagctaat tttttgtatt tttagtagag
 acagggcttc actatgttgg ccaggatggt ctcgaactcc tgacctcagg cgatctgcct
 gcctcggcct gggattacag atgtgggcca ctgtgcctgg ccAGATAAAC TACTTTGAAG
 TGGAAGAAAG Cttttttttt tttttgagac agggtctcac tgtattgccc aggctagagt
 gcagtggcac aatcttggct cactgcagcc ttgacctcct gggctcaggt gatcctccca
 cttcagccac ctggctaatt ttttttgtag agatggggtt ttgccatgtt gcccaggctg
 gtgtcaaact cctgagttca agcattctat gtcagctgcc caaaatgctg cggttacagg
 catgagccat tgccctcagc cTGTATCTTA ACCTTCCTTT AAATAGTCTG TCAAGTTACA
 CAGTGAGCAC AATTGCTTGT CTAGAACAGT GGGTAGttcT Cagtgtggcc cccagatgag
 tagcattagg aactgttacg aatgcaaact gtcatgtcta ccccagacct ttgagtcaga
 aatgggagtg ttggtctaaa aactgggctt tTTGggctgg gcgcagtggt gcacgcctgt
 aatcccagca cttgggaggc caaggcaggc ggatcacctg aggtcaggag ttcgagacca
 gcctggccaa catggtgaaa ccccgtctct actaaaaata ccaaaattag ccgggtgtgg
 tggcgagtac ctgtaatccc agctactcag gaggctgagg taggagaatc acttgaaccc
 gggaggcaga ggttgcagtg agccaagatg gcgccattgc cctccagcct gggcgacaga
 gcgagactcc atctcaaaaa aacaaacaaa aaaaCTGGGC TTTTTTTTTG GCAACCCTTG
 GGGAATAAAA ACCTATTATT TTCTTAAGGA CAAAGTATCC TGAAGCAAAA AAACCCAAAC
 AAA

  GeneView back to top
GeneView via analysis of contig annotation: TFRC transferrin receptor (p90, CD71)
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_029928->NM_003234
svfunction
HuRefNW_001838889->NM_003234
svfunction
CeleraNW_921873->NM_003234
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_029928->NM_003234->NP_003225409148reverseintron
HuRefNW_001838889->NM_003234->NP_003225121927reverseintron
CeleraNW_921873->NM_003234->NP_00322555343reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2239641 maps exactly once on NCBI human chromosome 3
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
3NW_001838889.1121927193090176minusTalt_assembly_8HuRefHuRefview200
3NW_921873.155343194373863minusTalt_assembly_1CeleraCeleraview200
3NT_029928.12409148197273811minusTref_assemblyreferencereferenceview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_029928
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC024937.21 NC_000003.10 AC016953.13

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss24608620AFD_EUR_PANELEuropean 46IG 0.217 0.478 0.304 1.000 0.457 0.543
AFD_AFR_PANELAfrican American 46IG 0.652 0.304 0.043 1.000 0.804 0.196
AFD_CHN_PANELAsian 48IG 0.667 0.292 0.042 1.000 0.812 0.188
ss52974650MCL_HISP-PANEL 84IG 0.357 0.524 0.119 0.479 0.619 0.381
MCL_AD-PANEL 44IG 0.636 0.273 0.091 0.317 0.773 0.227
MCL_ASIAN-PANEL 90IG 0.778 0.222 0.403 0.889 0.111
MCL_CEPH-PANEL 88IG 0.091 0.477 0.432 0.655 0.330 0.670
MCL_YORUB-PANEL 46IG 0.478 0.478 0.043 0.403 0.717 0.283

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.448+/-0.15226124000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNYES

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
HAPLOTYPE:Submission | Specifications | Sample HapSet | Sample Individual
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement

Revised: May 25, 2006 1:38 PM .