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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs179761          
refSNP ID: rs179761
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_021798.2:c.-16-454T>C
NM_181078.1:c.-16-454T>C
NM_181079.1:c.-16-454T>C
NT_010393.15:g.18754002T>C
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 ss1973865 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs179761 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
ss238970KWOK|OVLP-000621-313930rev/TA/Gctggctaatttttaaaacatttttgtagagcggcatcttgctatgttgcccaggctggtc06/30/0010/10/0379Genomic94 %
ss542816SC_JCM|AC002303.1_25880fwd/BC/Tgaccagcctgggcaacatagcaagatgccgctctacaaaaatgttttaaaaattagccag07/12/0010/10/0380Genomicunknown
ss1052854KWOK|OVLP-000804-64393fwd/BC/Tgaccagcctgggcaacatagcaagatgccgctctacaaaaatgttttaaaaattagccag09/02/0010/10/0386Genomic94 %
ss1973865KWOK|OVLP-000925-539173fwd/BC/Tgaccagcctgggcaacatagcaagatgccgctctacaaaaatgttttaaaaattagccag10/06/0010/10/0387Genomic94 %
ss4328506PGA-UW-FHCRC|IL21R-003767byFreqfwd/BC/Tgaccagcctgggcaacatagcaagatgccgctctacaaaaatgttttaaaaattagccag02/06/0204/07/04103Genomicunknown
ss10843782BCM_SSAHASNP|chr16.NT_010393.13_18713961fwd/BC/Tgaccagcctgggcaacatagcaagatgccgctctacaaaaatgttttaaaaattagccag06/30/0310/10/03116Genomicunknown
ss40667578ABI|hCV27077036fwd/BC/Tgaccagcctgggcaacatagcaagatgccgctctacaaaaatgttttaaaaattagccag07/17/0507/17/05126Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs179761|allelePos=760|totalLen=1162|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GCCTCATTAT TGGGCTAACC TTATCTTAAG TATTCAGCAG TGGTTAACTT TGTGGGTTAA
 CTTTGGATTT ATTATTCAGT AAGAAGCCAA TTTATTGATg gctgggtgca gtggctcatg
 cctgtaattc cagcactttg agaggctgag gtgggtggat cacctgtggc caggagttcg
 agaccagcct agtccacatg gcaaaaccct gtctctacta aaaatacaaa aattagccag
 gcgtggtggc ggccacctgt attcccagct acttgggaag ctgaggcagg agaatcgctt
 gaacctggga ggtagaggtt gcagtgagcc aagatcgggc cactgcactc cagcctgggc
 gatagagtga gactttgtct aaaaaataaa cataaaaaaG CCAATTTACT GGCTTTTTTT
 TACAACATGG ATGTTTATAG GAAGGAAGAT CCAAAATTGC TCCTCAGCAG ATCCCCCTTT
 CCAAACTAGT tttttctcct tttctctctc ccttcctctc tttttccctc cctctttctt
 tGTTAGATAG ATAAATACAC AAGTTTAATT TCACACACAA TGCTACATCA ATAGGCTCAG
 CAAGGGCAAA ATAGTCAGCA GTCTCCTCCC TCTTTAAATT CACCTTGTgc tgggcgtggt
 gactcatgcc tgtcatccca gcactttgag aggccgaggt aggaggatca tgtgatccca
 ggagtttgag accagcctgg gcaacatagc aagatgccg
 Y
 ctctacaaaa atgttttaaa aattagccag gcgtggtggc acgtgccttt ggtcccagct
 actcgggagg ctgatgcagg aggatcgctt gagcccagga ggttgaggct gcagtgagcc
 gtgattgcgc cattgcactc cagcctgggc aacagaacat gaccccatct ctaaaaatat
 taaaataaaa taataaaaca aaTTCACTTT GCATTTGTGA CGTGATGGGG CGGGGGCAGG
 AAGAAGGTGG GAGAAGGGAT TCTTGGGGTG AATCTGCCAT TTCTAAGAGG TGGGAGTTCT
 TGGGGTCATC CACAGGCCCC TCGGGATCTT GCATTTTTCT TAAGACAGTT CCAAGAATCA
 GGGGCAAGTC TGCCTGGGAA GAGACAGGAT GAGGGGGAGG CC

  GeneView back to top
GeneView via analysis of contig annotation: IL21R interleukin 21 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_010393->NM_021798
function
referenceNT_010393->NM_181078
function
referenceNT_010393->NM_181079
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010393->NM_021798->NP_06857018754002forwardintron
referenceNT_010393->NM_181078->NP_85156418754002forwardintron
referenceNT_010393->NM_181079->NP_85156518754002forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs179761 maps exactly once on NCBI human chromosome 16
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
16NW_001838401.1396910625529347plusTalt_assembly_8HuRefHuRefview759
16NW_926217.1473844026218236plusTalt_assembly_1CeleraCeleraview759
16NT_010393.151875400227348424plusTref_assemblyreferencereferenceview759

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010393 AC004525 AC004525.1
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss4328506PGA-AFRICAN-PANELAfrican American 48IG 0.125 0.333 0.542 0.371 0.292 0.708
PGA-EUROPEAN-PANELEuropean 46IG 0.174 0.304 0.522 0.150 0.326 0.674

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.427+/-0.177472600

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNYES

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Revised: May 25, 2006 1:38 PM .