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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs222859          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_015982.3:c.26G>T
NP_057066.2:p.Gly9Val
NT_010718.15:g.6795142C>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 ss12392760 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs222859 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
ss289417KWOK|OVLP-000621-262956rev/BG/Tgcgggatgagcgaggtggaggcggcagcggggctacagcggtccccgcggcgacggtgcc06/30/0010/10/0379Genomic97 %
ss575162SC_JCM|AC003688.1_96871fwd/TA/Cggcaccgtcgccgcggggaccgctgtagccccgctgccgcctccacctcgctcatcccgc07/12/0010/10/0387Genomicunknown
ss1240253KWOK|OVLP-000804-431078fwd/TA/Cggcaccgtcgccgcggggaccgctgtagccccgctgccgcctccacctcgctcatcccgc09/02/0010/10/0386Genomic97 %
ss12392760WI_SSAHASNP|chr17.NT_010718.13_6036685byFreqfwd/TA/Cggcaccgtcgccgcggggaccgctgtagccccgctgccgcctccacctcgctcatcccgc07/04/0310/25/06116Genomicunknown
ss14302499BCM_SSAHASNP|chr17.NT_010718.14_6038799fwd/TA/Cggcaccgtcgccgcggggaccgctgtagccccgctgccgcctccacctcgctcatcccgc11/05/0311/22/03119Genomicunknown
ss24811061SEQUENOM|sqnm197169rev/BG/Tgcgggatgagcgaggtggaggcggcagcggggctacagcggtccccgcggcgacggtgcc06/18/0406/18/04123cDNAunknown
ss28511642MGC_GENOME_DIFF|BC047760x37543500-C6038799Afwd/TA/Cggcaccgtcgccgcggggaccgctgtagccccgctgccgcctccacctcgctcatcccgc08/25/0408/25/04126cDNAunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs222859|allelePos=318|totalLen=580|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=126
 GCCGGGCTCC ACACTGCCCC TCCCCCAGCC CGCCGACCCC TCAGAGCCGC CCTGTGCGCG
 CCTGCCCCTC ACCCAGCACC GGCTTGTCCG CCTGACTCCG GGCCGGGGGG GCGGGGGTTC
 CCGAGACCGC CGTCGCCGGA TTGCCAGGGG TGCGGGAGCC CGGCGCCGAG GGGGTCCCAG
 CAGCGGGGCC CGAGGCGGCT ccgcccccgc cgcccgcccc gccgcctttc tgcggctccc
 ctgcgggcac cggtaccacc accgctacca cccctgccgc cgtcgcgggc accgtcgccg
 cggggaccgc tgtagcc
 M
 ccgctgccgc ctccacctcg ctcatcccgc cgggtccagt accggccaca gccgccaccg
 ccCCGGCCCC TCCCCCCGGC TCGCGAACCC ACCGCCCTGC TCGGTCCTCG CGCCCCGAGC
 CTCGCCCACA CGCCGGCAGC GGGCCCGGAG CCGAGGCCAA TGGCAGCCCG CTGCCGCCGC
 TCGCGCAGAC CCCGCCTCCC GACCACGGGC CAATCCCAGC CCAGCAGCAC CCCCGGACCG
 CACGCCGACC CCGCCTCCCG GA

  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
dbSTS GenBank
sqnm197169 NT_010718 AC026954 AC026954.3 BC047760
dbSNP Blast Analysis
UniGene Cluster ID
380691

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/C
 C/C
 HWP A
 C
ss12392760 HapMap-CEU European 120 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.667 0.317 0.017 0.479 0.825 0.175

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.160+/-0.233 350 234 0 0

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

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Revised: May 25, 2006 1:38 PM .