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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1189451          
refSNP ID: rs1189451
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/129
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_005845.3:c.3210+1830C>T
NT_009952.14:g.8811762G>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 ss1671130 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1189451 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
ss1671130KWOK|OVLP-000925-117892byFreqfwd/BC/Tgaggaatggaaaaacaaaatgtgatacgcagcataatggaatattatccagacttaaaaa10/05/0010/25/0687Genomic99 %
ss2569764SC_JCM|AC074260.2_52891fwd/BC/Tgaggaatggaaaaacaaaatgtgatacgcagcataatggaatattatccagacttaaaaa11/03/0010/10/0396Genomicunknown
ss3454144SC_JCM|AC074260.4_61787fwd/BC/Tgaggaatggaaaaacaaaatgtgatacgcagcataatggaatattatccagacttaaaaa09/24/0110/10/03106Genomicunknown
ss13196953SC_SNP|NT_009952.13_8811761rev/TA/Gtttttaagtctggataatattccattatgctgcgtatcacattttgtttttccattcctc10/22/0310/31/03119Genomicunknown
ss17499223CSHL-HAPMAP|CSHL-HuCC-200402.chr13.NT_009952.14_8811762rev/TA/Gtttttaagtctggataatattccattatgctgcgtatcacattttgtttttccattcctc02/19/0403/04/04120Genomicunknown
ss21128545SSAHASNP|WGSA-200403-chr13.chr13.NT_009952.14_8811762rev/TA/Gtttttaagtctggataatattccattatgctgcgtatcacattttgtttttccattcctc03/19/0403/19/04121Genomicunknown
ss40300641ABI|hCV1901925rev/TA/Gtttttaagtctggataatattccattatgctgcgtatcacattttgtttttccattcctc07/16/0507/16/05126Genomicunknown
ss75245104ILLUMINA|ILMN_Human_1M_rs1189451fwd/BC/Tgaggaatggaaaaacaaaatgtgatacgcagcataatggaatattatccagacttaaaaa08/28/0708/29/07129Genomicunknown
ss78329576HGSV|Cor12878_SNV_20070510.chr13_94520087rev/TA/Gtttttaagtctggataatattccattatgctgcgtatcacattttgtttttccattcctc10/17/0710/18/07129Genomicunknown
ss82834364HGSV|Cor18555_SNV_20070510.chr13_94520087rev/TA/Gtttttaagtctggataatattccattatgctgcgtatcacattttgtttttccattcctc11/27/0712/03/07130Genomicunknown
ss89806624BCMHGSC_JDW|JWB-0720215rev/TA/Gtttttaagtctggataatattccattatgctgcgtatcacattttgtttttccattcctc02/26/0802/28/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1189451|allelePos=593|totalLen=1277|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CCCTTCCCAC CCCTCTCCTC ACAACTCCCA ATATGGACAC ACATCCCCTG CACTCAGGGT
 GCCCTCCTTC TCCCCAAGCA CCTGTCTGCC TTGCTCTTAG TGTGCACCCT TTTCAGTCAG
 TTCAAGCATC TCTGCCTCTT TGAAACTATA TTCTCCACAT CATCTTATAG Attctttttt
 cgagacagag tcttgctctg tcgcccaggc tggagtgcaa tgtcacattc ccggcacact
 gcaacctcca cctcccaggt tcaagcgatt ttcctgcttc aacctccccc gtagctggga
 ttataggtgt gcaccaccat acccaactca tttttgaatt tttagtagag accaggtttt
 gccatgttgg ccatggctgg tctcgaactc ctgagctaaa gtgatccgcc caccttaacc
 tcccaaatca tgcctgggat tacaggcatg agccaccatg cctggccAGA TTCTTTAATG
 TAACATCTGT GGCCCAcccg tgttcataac agcattattt gcagtgagca gtaggtggaa
 gcagcccaag tgtccattga ctgaggaatg gaaaaacaaa atgtgatacg ca
 Y
 gcataatgga atattatcca gacttaaaaa gaaggtgatt ctgacacatg ctgacatgtg
 tgattctgac atggatgagc cctgaggaca ttatgctgag tgaattaggc cagacaccta
 aggacggtgc tataaggttc cacttacatg tgggtacctg gagtagttag tcatggagac
 agaaagtagg atggtgggcg gcaggggtag gggaatgggc attagtgttt aatgggtaca
 gagtttcagt tttacaagat aaatggagtt ttagagatgg atgatggtga cggttgccca
 acaacatgaa tgtatttaat ataattgaac tgaacatttt caagtgatta caatgatcaa
 ttttatgtta ctttaccaca atttgaaaaG TACATAAAGT ACCTTTTGTG TATTTTACCA
 CAATTTTTTT TTAAAGAAGA TAGCACGATG GCATGATTTA TAATTCTGGG TCAGCATCTC
 ACAGTACCCT GAGCCTCTTA AAGTCAGGGA GCATTTTATA TTCGTCTCTG TACCCCCAGA
 AAATGGCATG CTGCAGGGCA CATGGTGGGT GCCTGTGAGA GTGAGGGATA TGCACATACA
 AAGAAATCGG TAACAAAACA CACACGACAG CTCCCGCAAC AGCCCGTTCT CTGGGTGTCA
 GTGTTAGATA CTTTCGGAAC TGCT

  GeneView back to top
GeneView via analysis of contig annotation: ABCC4 ATP-binding cassette, sub-family C (CFTR/MRP), member 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_009952->NM_005845
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_009952->NM_005845->NP_0058368811762reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1189451 maps exactly once on NCBI human chromosome 13
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
13NW_001838084.21663717776320590plusTalt_assembly_8HuRefHuRefview592
13NW_925517.1882321976570018minusGalt_assembly_1CeleraCeleraview592
13NT_009952.14881176294520087minusGref_assemblyreferencereferenceview592

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_009952 AC022330 AL157818 AL157818.6
dbSNP Blast Analysis
GenBank HTGS Finished:
AL157818.12

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1671130HapMap-CEUEuropean 116IG 0.017 0.276 0.707 0.752 0.155 0.845
HapMap-HCBAsian 90IG 0.022 0.311 0.667 0.752 0.178 0.822
HapMap-JPTAsian 90IG 0.089 0.578 0.333 0.378 0.622
HapMap-YRISub-Saharan African 120IG 0.267 0.467 0.267 0.655 0.500 0.500

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.426+/-0.17827021000

  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

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Revised: May 25, 2006 1:38 PM .