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: rs659580          
refSNP ID: rs659580
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:83/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_006902.3:c.241+296T>C
NM_022716.2:c.241+296T>C
NT_004487.18:g.21124251T>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 ss76888677 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs659580 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
ss832730SC_JCM|AL162399.4_158627fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg07/27/0005/28/0483Genomicunknown
ss1846209KWOK|OVLP-000925-724985fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg10/05/0010/10/0387Genomic97 %
ss3195244YUSUKE|IMS-JST011166byFreqrev/TA/Gccgcgtgcgggatgaaccgagccggtgcctgccgaagtaaagagagtccgccgcggacag08/07/0110/10/0398Genomicunknown
ss13006840SC_SNP|NT_004668.15_17004455fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg10/22/0310/31/03119Genomicunknown
ss16452861CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_004668.16_9139368fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg02/17/0403/04/04120Genomicunknown
ss17371881CSHL-HAPMAP|CSHL-HuCC-200402.chr1.NT_004668.16_9139368fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg02/19/0403/04/04120Genomicunknown
ss20522977SSAHASNP|WGSA-200403-chr1.chr1.NT_004668.16_9139368fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg03/18/0403/18/04121Genomicunknown
ss43988076ABI|hCV2480865byFreqfwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg07/18/0511/03/06126Genomicunknown
ss66591480ILLUMINA|HumanHap300v1.1_rs659580fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg11/09/0611/09/06127Genomicunknown
ss67477561ILLUMINA|HumanHap550v1.1_rs659580fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg11/14/0611/14/06127Genomicunknown
ss67833805ILLUMINA|HumanHap650Yv1.0_rs659580fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg11/14/0611/14/06127Genomicunknown
ss70875946ILLUMINA|HumanHap550v3.0__rs659580fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg04/20/0703/31/08130Genomicunknown
ss71465658ILLUMINA|HumanHap650Yv3.0_rs659580fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg04/23/0704/23/07127Genomicunknown
ss74917241ILLUMINA|ILMN_Human_1M_rs659580fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg08/28/0708/29/07129Genomicunknown
ss76787428AFFY|AFFY_6_1M_SNP_A-8648957fwd/BC/Tctctctttacttcggcaggcaccggctcggtt08/28/0708/30/07129Genomicunknown
ss76888677SI_EXO|NT_004487.18_21124251fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg09/20/0709/20/07129Genomicunknown
ss79002188HGSV|Cor18507_SNV_20070510.chr1_167365554fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg10/19/0710/21/07129Genomicunknown
ss79227605ILLUMINA|HumanHap300v2.0_rs659580fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg04/18/0711/18/07130Genomicunknown
ss83510360KRIBB_YJKIM|KHS478619fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg12/04/0712/05/07130Genomicunknown
ss83873537HGSV|Cor19240_SNV_20070510.chr1_167365554fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg11/30/0712/05/07130Genomicunknown
ss87866370BCMHGSC_JDW|JWB-0144326fwd/BC/Tctgtccgcggcggactctctttacttcggcaggcaccggctcggttcatcccgcacgcgg02/26/0802/26/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs659580|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GGGACATGGT GGCGGCACAG GCGGATGAGA ACGTGGGCGA GGCTGGCCGG AGCCTGCTGG
 AGTCGCCGGG ACTCACCAGC GGCAGCGACA CCCCGCAGCA GGACAGTGAG TGAGGGGCGC
 ATGCCCACGG GGGTGTGTGC CCGGGACAGA GGGCGGGGAC CCGTGTAGGG CAGCTAGAGC
 CCGTCCGCGG CCAGAAAGAC AAGGTCCTGG GACCAGGAGA GGTGATGGCA GACTTCAAAG
 GAAGGGCCAG TCACAGGGGA AACCAGATGA GAAAAGCGGG TCTCGGCCGA GGGCATAGCC
 AAGGAGGACG CTGGAGAGAG GCTCCAAGGT CCGGGGACAC TCCGAGGCCC TGCGGTCTCA
 GGCAGGGACT CTGTCCGCGG CGGACTCTCT TTACTTCGGC
 Y
 AGGCACCGGC TCGGTTCATC CCGCACGCGG GGCGGCGGGG CTGGGCTGGG AAAAGGTCTT
 AGCGGGGTGC AAACTCAGAG AGCCAGCGCT GTTTGGGAAA GCAGCAGGTT AAAGATGCTG
 AGTCGGGTTG GAAGGGCTTC TCTCGGGCAG CGTATGACGG CTTGAGGGAG GGCACCAGGC
 ACAGGGAGCA GGACTTGGCG CTGCTCAGGC TGCACTCTCC ACGCGGGCAC CGTAAGGCCG
 GGCGCGACCG GGAGGCCCCG AGAGAACGCC CGGCCCCAGA CGCTGGAGCT GCTCTCTGCC
 CCCTGCTGTT GCCTCTACCG CAAATGGGTT TGAGACTGGC AGAGTCAAAA GCCCGGCTGG
 CTTGGGAAAA CTCGGGCCAA GCAAAGGGAA TGTCCTTTAA

  GeneView back to top
GeneView via analysis of contig annotation: PRRX1 paired related homeobox 1
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_004487->NM_006902
function
referenceNT_004487->NM_022716
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_004487->NM_006902->NP_00883321124251forwardintron
referenceNT_004487->NM_022716->NP_07320721124251forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs659580 maps exactly once on NCBI human chromosome 1
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
1NW_001838533.235247490141857761minusGalt_assembly_8HuRefHuRefview300
1NW_926128.18998271143743512plusCalt_assembly_1CeleraCeleraview300
1NT_004487.1821124251168900520plusTref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
Z97200.1 Z97200 Z97200.1
dbSNP Blast Analysis
GenBank HTGS Finished:
Z97200.1

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss3195244JBIC-allele 1484AF 0.517 0.483
ss43988076HapMap-CEUEuropean 120IG 0.517 0.450 0.033 0.200 0.742 0.258
HapMap-HCBAsian 90IG 0.244 0.444 0.311 0.479 0.467 0.533
HapMap-JPTAsian 88IG 0.273 0.500 0.227 1.000 0.523 0.477
HapMap-YRISub-Saharan African 120IG 1.000 1.000
AoD_African_American 90AF 0.990 0.010
AoD_Caucasian 92AF 0.830 0.170

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.411+/-0.19127021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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 .