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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1551888          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_000695.3:c.155G>A
NM_001031615.1:c.155G>A
NP_000686.2:p.Ser52Asn
NP_001026786.1:p.Ser52Asn
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 ss2394820 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1551888 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
ss2394820TSC-CSHL|TSC0435804byFreqfwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg10/20/0005/16/0488Genomic95 %
ss3172759WIAF-CSNP|WIAF-14065byFreqrev/TA/Gtgctcctggtgggcaccctccccgcagggattgcgtggtgctgaagccgtcagaaatcag06/19/0104/07/04102cDNAunknown
ss4417273LEE|e456689rev/TA/Gtgctcctggtgggcgccctcgccgcagggattgcgtggtgctgaagccgtcagaaatcag04/26/0210/10/03126cDNAunknown
ss5472161TSC-CSHL|TSC0871780fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg09/21/0210/10/03108Genomicunknown
ss10672585BCM_SSAHASNP|chr11.NT_033903.5_12534258fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg06/29/0310/10/03116Genomicunknown
ss16538024CSHL-HAPMAP|CSHL-HuAA-200402.chr11.NT_033903.6_12606911fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg02/17/0403/04/04120Genomicunknown
ss20769714SSAHASNP|WGSA-200403-chr11.chr11.NT_033903.6_12606911fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg03/19/0403/19/04121Genomicunknown
ss65725737ILLUMINA|Human1-rs1551888fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg10/10/0610/10/06127Genomicunknown
ss66640284ILLUMINA|HumanHap300v1.1_rs1551888fwd/TC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg11/09/0611/09/06127Genomicunknown
ss67131775ILLUMINA|HumanHap550v1.1_rs1551888fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg11/14/0611/14/06127Genomicunknown
ss67471460ILLUMINA|HumanHap650Yv1.0_rs1551888fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg11/14/0611/14/06127Genomicunknown
ss70442671ILLUMINA|HumanHap300v2.0_rs1551888fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg04/18/0711/18/07127Genomicunknown
ss70631836ILLUMINA|HumanHap550v3.0__rs1551888fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg04/20/0703/30/08130Genomicunknown
ss71181927ILLUMINA|HumanHap650Yv3.0_rs1551888fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg04/23/0704/23/07127Genomicunknown
ss75530576ILLUMINA|ILMN_Human_1M_rs1551888fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg08/28/0708/29/07129Genomicunknown
ss83500374HGSV|Cor18956_SNV_20070510.chr11_67190445fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg11/30/0712/05/07130Genomicunknown
ss83831437KRIBB_YJKIM|KHS553210fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg12/04/0712/05/07130Genomicunknown
ss97393825HUMANGENOME_JCVI|1103649712062fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg03/29/0803/29/08130Genomicunknown
ss1105994531000GENOMES|CEU.trio.12.15.2008_2562955_chr11_67190445fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg12/15/0812/17/08130Genomicunknown
ss1147290331000GENOMES|NA19240_2008_12_16_2308701_chr11_67190445fwd/BC/Tctgatttctgacggcttcagcaccacgcaatccctgcaggggcagatggggacgtcgttg12/18/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1551888|allelePos=448|totalLen=749|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTGCTGCAAT GTGCCCAGGG CGTGGCCTAT GCAGGCAGAC GGACTCTGTG CCAGCTCCAG
 CTCCCCACGT GCCCCCACTG CTGGCCCCAG CCTCCTCCCT CCACAACCCT CCCACCCTCT
 CTCCTGATGA TCCCCTCCAC CTACTCTGGG ACCCTGGCCT GGCCCCCTCA CCTGTGAAGA
 AGATGTAGTC CAACTTGTGC TCTAGCAGCT GCCCTGTCTC CTGGGGTCCG CCCAGCACCA
 CGGCAAAGCA GCTCTGCAAG GTGGAATGAG AGGCTCGGGG CGGGCTCGGG GCCAGCCGGG
 CCTCCTCAGC CCACAGGGGT GATATATGGG GACGTCGGGC ACTGCTGGGG CAGGGCCACC
 CTCACCTGGT CCAGGTACTG GGGCAGCACC TCAGCCAGGA CCTTCTCTGT GCCCTGGCTG
 ATTTCTGACG GCTTCAGCAC CACGCAA
 Y
 TCCCTGCAGG GGCAGATGGG GACGTCGTTG GGGGAGCCCA GGGTCCCCAT GCCCAACCAG
 GGGCTGGGCT CAGAGGGCAT GTGAGGCCCA GGGTACCTCA GAGCAAGATT CCAGGGGCCT
 CTTTGGGAGG GGCTACTGGG CGGGGAGAGC ATGGGGTTCG GAACGCCCTC CTCACCTGCG
 GCGAGGGCGC CCACCAGGAG CACCAGGGTC AGGTTCAGTG GGTAGTTCCA GGGTGCGATG
 ATGAGGACCA GGCCAAAGGG TTCCTTCCAG ATGAAGACCG AGTCCAGCTT CATGAACTGA
 G

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
U37519 ABBA01024026 Hs.87539
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss2394820 CEPH 184 AF 0.160 0.840
HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 84 IG 0.214 0.786 0.439 0.107 0.893
HapMap-JPT Asian 86 IG 0.140 0.860 0.655 0.070 0.930
HapMap-YRI Sub-Saharan African 120 IG 0.100 0.400 0.500 0.300 0.700
ss3172759 WIAF-CSNP-MITOGPOP5 multiple 52 IG 0.115 0.038 0.846 0.001 0.135 0.865
Concordant Genotype Total Sample C/C C/T T/T
ss2394820 1206 26 251 906
ss3172759 25
ss97393825 1 1
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs1551888 1227 26 251 907
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
467 ss3172759 G/G WIAF-CSNP WIAF-CSNP-MITOGPOP5 CL6 06.18.01-a
467 ss2394820 T/T CSHL-HAPMAP HapMap-CEU NA12006 CEPH1420.12 r27_ch11_CEU_illumina:human_1m_beadchip 795768
Genotype data submitted for1234 samples from1227 individualsIndividual with multiple genotypes submission:7

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN YES YES

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Revised: May 25, 2006 1:38 PM .