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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1888087          
refSNP ID: rs1888087
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:92/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_015985.2:c.*168A>C
NT_011387.8:g.793435T>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 ss8446066 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1888087 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
ss2768127TSC-CSHL|TSC0907955byFreqfwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg01/02/0104/07/0492Genomicunknown
ss6648344WI_SSAHASNP|NT_011387.8_793435fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg02/12/0310/10/03111Genomicunknown
ss8446066SC_SNP|NT_011387.8_793435byFreqfwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg04/17/0310/30/04114Genomicunknown
ss10953453BCM_SSAHASNP|chr20.NT_011387.8_793435fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg06/30/0310/10/03116Genomicunknown
ss21763053SSAHASNP|WGSA-200403-chr20.chr20.NT_011387.8_793435fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg03/20/0403/20/04121Genomicunknown
ss66773352ILLUMINA|HumanHap300v1.1_rs1888087fwd/TG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg11/09/0611/09/06127Genomicunknown
ss67203749ILLUMINA|HumanHap550v1.1_rs1888087fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg11/14/0611/14/06127Genomicunknown
ss67595944ILLUMINA|HumanHap650Yv1.0_rs1888087fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg11/14/0611/14/06127Genomicunknown
ss68417599CSHL-HAPMAP|sanger:assay:4481173:1byFreqfwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg01/11/0701/16/07127NAunknown
ss70681975ILLUMINA|HumanHap550v3.0__rs1888087rev/TA/Cccagaagtccagaagggtcatctgccccccactcccctccgtctgtgacatggagggtgt04/20/0703/30/08130Genomicunknown
ss71245787ILLUMINA|HumanHap650Yv3.0_rs1888087fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg04/23/0704/23/07127Genomicunknown
ss75912664ILLUMINA|ILMN_Human_1M_rs1888087fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg08/28/0708/29/07129Genomicunknown
ss76886406SI_EXO|NT_011387.8_793435fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg09/20/0709/20/07129Genomicunknown
ss78547958HGSV|Cor12878_SNV_20070510.chr20_801435fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg10/17/0710/19/07129Genomicunknown
ss79099087ILLUMINA|HumanHap300v2.0_rs1888087fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg04/18/0711/18/07130Genomicunknown
ss80113903HGSV|Cor18507_DIV_20070510.chr20_801434-801436_1fwd/-/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg11/23/0711/24/07130Genomicunknown
ss83727020HGSV|Cor18555_SNV_20070510.chr20_801435fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg11/27/0712/05/07130Genomicunknown
ss83904295KRIBB_YJKIM|KHS569270fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg12/04/0712/06/07130Genomicunknown
ss91613918BCMHGSC_JDW|JWB-1409399fwd/BG/Tacaccctccatgtcacagacggaggggagtggggggcagatgacccttctggacttctgg02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1888087|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 GGTCATTAGA ACCTAGAAGT GGTGAAGTGT GAAGGGGAAA TAATGATTAA CCCACCCACT
 AAGGGGTGGA TGCAGCCCCT TCAGACTTGA AAAGAAAGTT CAAGGACATC TCAAGACTAG
 AAAATCTTGG AACAGGAGCT TAGAATGGGA GATGGCCTTC TTGCCAATCC AAGGGAGAGA
 ACCTGGGCCA TCTGGGCAGC TTCCGATGTG CAAATACATT CCCACCTGCC TGCAACCCCA
 CCATTGGTCA TGGGAATCAA GTTTGGTCTG TTCTCAGCCC ATTCAAGGTA CTGTGACCCT
 CAGGCAGGGA GCCCCTGAAG GGGGAGGGAG AGAAGAGGGG CGAGGACTAC ATCAGAGGGA
 TGGGCCCCGA ACACCCTCCA TGTCACAGAC GGAGGGGAGT
 K
 GGGGGGCAGA TGACCCTTCT GGACTTCTGG GTCAAGGAGG GCTGGCTCAG GAAGCCCAGG
 GTGTCAGGGA AGGCGGTGGC ACAGTGTCTT GCATCTGGGT CCAGGTTGTC CAGGAGTGCC
 AAGTCCGAGC TTCTCCTGTG TGGTCCAGCC TCTGGCACAG CTGCTCGTTA GATGTCCAAA
 GGCCGTATCA TCATGCGAGA GGCACGCAGT GAGTAGCTGG GGCCCTTGAA GTAGTGCCAG
 CGGATGCCGT CCATCTTGTA CTTGTTGTCG GGAGCGTGGT AGTAGACGCC GTTGAGGTTT
 GACAGGCCAC AGGCGTCAAA CCACCACCCT GGTGGAAGAG GGAGGACAGG CGCTTGGTGG
 AGGTGGGAGC CCAGCCAGTG GCAAGAGGGC AGCCCCTGTG

  GeneView back to top
GeneView via analysis of contig annotation: ANGPT4 angiopoietin 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_011387->NM_015985
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011387->NM_015985->793435reverse17833' UTR

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1888087 maps exactly once on NCBI human chromosome 20
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
20NT_011387.8793435801435plusTref_assemblyreferencereferenceview400
20NW_001838652.1805786805786plusGalt_assembly_8HuRefHuRefview400
20NW_927317.1806880949704plusGalt_assembly_1CeleraCeleraview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011387.8
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank HTGS Finished:
NM_015985.2 AL161939.10
UniGene Cluster ID
278973

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceG/G
G/T
T/T
HWPG
T
ss2768127WICGR8_asian_pooled 84AF 1.000
WICGR6_caucasian_pooled 96AF 0.890 0.110
ss8446066HapMap-CEUEuropean 120IG 0.800 0.183 0.017 0.752 0.892 0.108
HapMap-HCBAsian 90IG 0.867 0.133 0.933 0.067
HapMap-JPTAsian 90IG 0.756 0.244 0.878 0.122
HapMap-YRISub-Saharan African 120IG 0.317 0.583 0.100 0.371 0.608 0.392

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.299+/-0.24527021000

  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:  NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .