Skip to main content
NCBI
 dbSNP
PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
transparent GIF
Spacer gif
BUILD 130
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs2857663          **clinically associated**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:link to VariationViewer
HGVS Names
NG_008352.1:g.7095C>T
NM_002282.2:c.445T>C
NM_002282.3:c.445C>T
NP_002273.3:p.Arg149Cys
NT_029419.11:g.14856394G>A
XM_001713687.1:c.445C>T
XM_001719155.1:c.445C>T
XP_001713739.1:p.Arg149Cys
XP_001719207.1:p.Arg149Cys
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 ss43565339 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2857663 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
ss4045605SC_JCM|Y19208.1_3474fwd/BC/Tctggagacaaagctgcagttctaccaaaacgcgagtgctgccagagtaacctggagcccc09/26/0110/25/06100Genomicunknown
ss4927720YUSUKE|IMS-JST092767byFreqfwd/BC/Tctggagacaaagctgcagttctaccaaaacgcgagtgctgccagagtaacctggagcccc07/29/0210/10/03108Genomicunknown
ss17451464CSHL-HAPMAP|CSHL-HuCC-200402.chr12.NT_029419.10_14856394rev/TA/Gggggctccaggttactctggcagcactcgcgttttggtagaactgcagctttgtctccag02/19/0403/04/04120Genomicunknown
ss24342402PERLEGEN|afd4303809byFreqrev/TA/Gggggctccaggttactctggcagcactcgcgttttggtagaactgcagctttgtctccag08/10/0409/13/04124Genomicunknown
ss43565339ABI|hCV26278223byFreqrev/TA/Gggggctccaggttactctggcagcactcgcgttttggtagaactgcagctttgtctccag07/18/0511/03/06126Genomicunknown
ss66272208AFFY|SNP_A-4302557byFreqfwd/BC/Tgcagttctaccaaaacgcgagtgctgccagag10/27/0608/14/07127Genomicunknown
ss76417075AFFY|AFFY_6_1M_SNP_A-4302557fwd/BC/Tgcagttctaccaaaacgcgagtgctgccagag08/28/0708/30/07130Genomicunknown
ss77780693HGSV|Cor12156_SNV_20070510.chr12_50999355rev/TA/Gggggctccaggttactctggcagcactcgcgttttggtagaactgcagctttgtctccag10/09/0710/14/07129Genomicunknown
ss80700019HIFD-CURATED-RECORDS|HIFD_KRT83:c.445T>Cfwd/BC/Tctggagacaaagctgcagttctaccaaaacgcgagtgctgccagagtaacctggagcccc11/26/0702/26/08130Genomicunknown
ss81893694KRIBB_YJKIM|KHS156781fwd/BC/Tctggagacaaagctgcagttctaccaaaacgcgagtgctgccagagtaacctggagcccc11/30/0712/01/07130Genomicunknown
ss1119434611000GENOMES|CEU.trio.12.15.2008_2736554_chr12_50999355rev/TA/Gggggctccaggttactctggcagcactcgcgttttggtagaactgcagctttgtctccag12/15/0812/17/08130Genomicunknown
ss1135455921000GENOMES|NA19240_2008_12_16_2459762_chr12_50999355rev/TA/Gggggctccaggttactctggcagcactcgcgttttggtagaactgcagctttgtctccag12/18/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2857663|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTCTTCAAGC ATTTTCCATG ACACCAGGTA AACTGACTTA GAAGAGATTA ACTCCCAGGA
 AGAACTTCCA GGTGGTGAAC TGGTTAAGCC CTGGTGGCAT TTTTGAGAGA GATGACATAA
 CGCCTTCCAG GGAAGACTCT GGGTCAGAGA GTTGGGGGCT TTCAGGCCCT CGTGCTGGGA
 ACCCCTCTTG TCCTCTGATG CTGCAAGAAG AGGTTCTTAG GCTCTGCCTC TGGGTGGCAG
 GTGCGCTTCC TGGAGCAGCA GAACAAGCTG CTGGAGACAA AGCTGCAGTT CTACCAAAAC
 Y
 GCGAGTGCTG CCAGAGTAAC CTGGAGCCCC TGTTTGCTGG CTACATCGAG ACTCTGCGGC
 GGGAGGCCGA GTGCGTGGAG GCTGACAGTG GGAGGCTGGC CTCAGAGCTC AACCACGTGC
 AGGAGGTGCT GGAGGGCTAC AAGAAGAAGT GAGTGTGGGC AGGAGGGGTT CTGGGCACAG
 GAAATAGCAT GGTGGCAGCT CCCTGAGCCC GGAGGAGTAT CCAGTCTGCA GCTGGCATCT
 CTGCCTGAGA GTGGAGAAGA ACCTGTACCC CCTGTTTGAG ACACAGGGGT CCCTTGGGTG

  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
Y19208 AP002519
dbSNP Blast Analysis
UniGene Cluster ID
182506

  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
ss24342402 AFD_EUR_PANEL European 48 IG 0.625 0.375 0.273 0.812 0.188
AFD_AFR_PANEL African American 46 IG 0.826 0.174 0.655 0.913 0.087
AFD_CHN_PANEL Asian 48 IG 0.875 0.125 0.752 0.938 0.062
ss43565339 HapMap-CEU European 120 IG 0.683 0.317 0.150 0.842 0.158
HapMap-HCB Asian 90 IG 0.867 0.133 0.655 0.933 0.067
HapMap-JPT Asian 88 IG 0.795 0.205 0.479 0.898 0.102
HapMap-YRI Sub-Saharan African 120 IG 0.717 0.250 0.033 0.655 0.842 0.158
ss4927720 JBIC-allele 1456 AF 0.911 0.089
ss66272208 HapMap-CEU European 118 GF 0.678 0.322 0.839 0.161
HapMap-HCB Asian 90 GF 0.867 0.133 0.933 0.067
HapMap-JPT Asian 90 GF 0.800 0.200 0.900 0.100
HapMap-YRI Sub-Saharan African 120 GF 0.717 0.250 0.033 0.842 0.158
ss76417075 ICMHP 10 IG 0.800 0.200 0.900 0.100

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.218+/-0.248 1268 1052 275 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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 .