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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6887898          
refSNP ID: rs6887898
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/129
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_000949.2:c.-106+39622C>T
NT_006576.15:g.35163505G>A
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 ss10246781 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6887898 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
ss10246781BCM_SSAHASNP|chr5.NT_006576.13_17616941byFreqfwd/TA/Gaaaaaaaaaaaaagttctgctttggcctaacaatcagttgctttttcgttgaaacaattt06/27/0310/25/06116Genomicunknown
ss14659948WI_SSAHASNP|chr5.NT_006576.14_17642854fwd/TA/Gaaaaaaaaaaaaagttctgctttggcctaacaatcagttgctttttcgttgaaacaattt11/05/0311/22/03119Genomicunknown
ss19620036CSHL-HAPMAP|CSHL-HuDD-200402.chr5.NT_006576.14_17642854fwd/TA/Gaaaaaaaaaaaaagttctgctttggcctaacaatcagttgctttttcgttgaaacaattt02/20/0403/04/04120Genomicunknown
ss42427930ABI|hCV29959542fwd/TA/Gaaaaaaaaaaaaagttctgctttggcctaacaatcagttgctttttcgttgaaacaattt07/18/0507/18/05126Genomicunknown
ss77771509HGSV|Cor12156_SNV_20070510.chr5_35226505fwd/TA/Gaaaaaaaaaaaaagttctgctttggcctaacaatcagttgctttttcgttgaaacaattt10/09/0710/14/07129Genomicunknown
ss78723690HGSV|Cor12878_SNV_20070510.chr5_35226505fwd/TA/Gaaaaaaaaaaaaagttctgctttggcctaacaatcagttgctttttcgttgaaacaattt10/17/0710/20/07129Genomicunknown
ss85865285HGSV|Cor19129_SNV_20070510.chr5_35226505fwd/TA/Gaaaaaaaaaaaaagttctgctttggcctaacaatcagttgctttttcgttgaaacaattt12/06/0712/10/07130Genomicunknown
ss93058756BCMHGSC_JDW|JWB-1962670fwd/TA/Gaaaaaaaaaaaaagttctgctttggcctaacaatcagttgctttttcgttgaaacaattt02/26/0803/03/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6887898|allelePos=825|totalLen=1025|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TTTCCATGAC CCCAAGCCCT TCAAATAATA GTGAAAATCA aggaaactga gcccagaaag
 gtcaaaccac ttgtctaaag ccgcacagct ttggggcagc aggatcagag tagacatcct
 gcttcccagt ccagggtttt cctgctGGAG CACAGGAGCC TCCCTGTTTA CCCAGTGAAA
 TGAGATGCAG GAATTCAAGA GGCAAGAGGG AGAGAGCCCC ATTGCCTTGG ACTTGGAGGT
 AAGGGAGTCC ATGCTTCTGA GGTGAGTCGg cttccagcac tatgagacaa cacatttctg
 ttgtttaagc cacccagttg tggtactttg ttatggcagc cccagcaaac cagtacaGGG
 GGACAAtata attatcccat tttacatgtg gaaaccaagg cacaaagaga ttaagttctt
 ccccaatgcc ccacagcgaa cacttagcag gcagtttgct ccagaatgtg ccctcttaac
 tacagtacta AAAATAATTC Tggctgggca tggtggctca cacctgtaat cccagcactt
 cggaaggctg atgcgagtgg atcgcttgag gtcaggagtt caagaccagc ctggccaacg
 tggcaaaacc ctgtctctac taaaaataca aaaattagct gggcatagtg gcaggtgcct
 gtaatcctag ctactcggaa gtctgaggca ggagaatcgc tagaactggg gagatggagg
 ttgcagtgag ccgagattgt gagattgtgc cactgcactc cagcatgggt gacagactga
 gactttgcct caggaaaaaa aaaaaaaGTT CTGCTTTGGC CTAA
 R
 CAATCAGTTG CTTTTTCGTT GAAACAATTT TTAATTTCAA CATAATCCTA TCATAATCAG
 AAAAGAATAA GTGTACACTT TAGGGGTGAA TGATCTTTCC CTACTGAGCC CATCTTATTC
 TGCTGCACTG TGCTAGAGCA TCTTGACCAC TGTGTATCTA CTTATAACCA AAGACAAATC
 TTCTTTCCAA CAGAGGCTCT

  GeneView back to top
GeneView via analysis of contig annotation: PRLR prolactin receptor
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_006576->NM_000949
function
HuRefNW_001838932->NM_000949
function
CeleraNW_922596->NM_000949
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_006576->NM_000949->NP_00094035163505reverseintron
HuRefNW_001838932->NM_000949->NP_000940517725forwardintron
CeleraNW_922596->NM_000949->NP_000940783386reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6887898 maps exactly once on NCBI human chromosome 5
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
5NW_922596.178338635072872plusGalt_assembly_1CeleraCeleraview824
5NW_001838932.251772535139565minusTalt_assembly_8HuRefHuRefview824
5NT_006576.153516350535226505plusGref_assemblyreferencereferenceview824

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_006576
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
ss10246781HapMap-CEUEuropean 114IG 0.825 0.158 0.018 0.479 0.904 0.096
HapMap-HCBAsian 88IG 0.250 0.477 0.273 1.000 0.489 0.511
HapMap-JPTAsian 90IG 0.222 0.556 0.222 0.479 0.500 0.500
HapMap-YRISub-Saharan African 118IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.371+/-0.21927021000

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

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Revised: May 25, 2006 1:38 PM .