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: rs17594721          
refSNP ID: rs17594721
Organism:human (Homo sapiens)
Molecule Type:HASH(0x1197f80)
Created/Updated in build:123/129
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_001083962.1:c.369+4793T>C
NM_003199.2:c.369+4793T>C
NT_025028.13:g.856756A>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 ss114441801 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17594721 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
ss24564541PERLEGEN|afd3373548byFreqfwd/TA/Gagttttctggttttcgtaggcatgaaaaagtgctcacaatatggttcatgtacattgcta08/10/0409/13/04123Genomicunknown
ss66772539ILLUMINA|HumanHap300v1.1_rs17594721fwd/BA/Gagttttctggttttcgtaggcatgaaaaagtgctcacaatatggttcatgtacattgcta11/09/0611/09/06127Genomicunknown
ss67189293ILLUMINA|HumanHap550v1.1_rs17594721fwd/TA/Gagttttctggttttcgtaggcatgaaaaagtgctcacaatatggttcatgtacattgcta11/14/0611/14/06127Genomicunknown
ss67568142ILLUMINA|HumanHap650Yv1.0_rs17594721fwd/TA/Gagttttctggttttcgtaggcatgaaaaagtgctcacaatatggttcatgtacattgcta11/14/0611/14/06127Genomicunknown
ss70667414ILLUMINA|HumanHap550v3.0__rs17594721rev/BC/Ttagcaatgtacatgaaccatattgtgagcactttttcatgcctacgaaaaccagaaaact04/20/0703/30/08130Genomicunknown
ss71229356ILLUMINA|HumanHap650Yv3.0_rs17594721fwd/TA/Gagttttctggttttcgtaggcatgaaaaagtgctcacaatatggttcatgtacattgcta04/23/0704/23/07127Genomicunknown
ss75797534ILLUMINA|ILMN_Human_1M_rs17594721fwd/TA/Gagttttctggttttcgtaggcatgaaaaagtgctcacaatatggttcatgtacattgcta08/28/0708/29/07129Genomicunknown
ss79091917ILLUMINA|HumanHap300v2.0_rs17594721fwd/TA/Gagttttctggttttcgtaggcatgaaaaagtgctcacaatatggttcatgtacattgcta04/18/0711/18/07130Genomicunknown
ss85393214KRIBB_YJKIM|KHS988162fwd/TA/Gagttttctggttttcgtaggcatgaaaaagtgctcacaatatggttcatgtacattgcta12/04/0712/09/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17594721|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=|build=130
 CTTTCCAGAT ATACAGGCCT AGAACAGTGA AGTCACCAGG TGAATGAGAC GATTCAACCC
 CCCAAAAAGT CAGAGTGGGT GTCTCTCCAC GGTATGACTT TGGTGTCCTT CCAGAGCCTG
 CACAGCATGT TAGAAGGAAG AGCTTCCAAA GGACTTTTTT GGGAGAGTGC AGTTTTCTGG
 TTTTCGTAGG CATGAAAAAG
 R
 TGCTCACAAT ATGGTTCATG TACATTGCTA TTCAGACCTT ACTCCCTCAA AATGGCTTCC
 AAAAGTGATG CTGAGGAAAG AAACACTAGG TCATTGCAAT TTTTGCCCTG CTAGGCACAT
 GGTACACATT CAGGATAAAG CAGACATGGT CCCTGCCCTC CAGGAGTTTA CAGAATCCTG
 TGGAAATCAG CATGCAACAA

  GeneView back to top
GeneView via analysis of contig annotation: TCF4 transcription factor 4
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_025028->NM_001083962
function
referenceNT_025028->NM_003199
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_025028->NM_001083962->NP_001077431856756reverseintron
referenceNT_025028->NM_003199->NP_003190856756reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs17594721 maps exactly once on NCBI human chromosome 18
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
18NW_001838469.185944649776097plusAalt_assembly_8HuRefHuRefview100
18NW_927106.1837612449782541plusAalt_assembly_1CeleraCeleraview100
18NT_025028.1385675651216890plusAref_assemblyreferencereferenceview100

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000018.5
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss24564541AFD_EUR_PANELEuropean 48IG 0.792 0.167 0.042 0.251 0.875 0.125
AFD_AFR_PANELAfrican American 46IG 0.870 0.087 0.043 0.050 0.913 0.087
AFD_CHN_PANELAsian 48IG 1.000 1.000
HapMap-CEUEuropean 120IG 0.917 0.067 0.017 0.025 0.950 0.050
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 0.567 0.383 0.050 0.752 0.758 0.242

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.147+/-0.22833226090

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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 .