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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs179208          
refSNP ID: rs179208
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/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NT_010393.15:g.10620013C>G
XM_001129496.2:c.89-3061C>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 ss1853278 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs179208 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
ss238283KWOK|OVLP-000621-296286fwd/TC/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag06/30/0010/10/0379Genomic94 %
ss1268154KWOK|OVLP-000804-20352fwd/TC/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag09/02/0010/10/0386Genomic94 %
ss1853278KWOK|OVLP-000925-508700byFreqfwd/TC/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag10/06/0004/07/0487Genomic94 %
ss3534069SC_JCM|AC003003.1_112414fwd/TC/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag09/24/0110/10/03100Genomicunknown
ss10813832BCM_SSAHASNP|chr16.NT_010393.13_10580152fwd/TC/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag06/30/0310/10/03116Genomicunknown
ss16135018SC_SNP|NT_010393.14_10619267fwd/TC/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag11/18/0311/22/03120Genomicunknown
ss20015831CSHL-HAPMAP|CSHL-HuFF-200402.chr16.NT_010393.14_10619267fwd/TC/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag02/21/0403/04/04120Genomicunknown
ss24524224PERLEGEN|afd3702404byFreqfwd/TC/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag08/10/0409/13/04123Genomicunknown
ss43913303ABI|hCV3268497fwd/C/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag07/18/0507/18/05126Genomicunknown
ss77745568HGSV|Cor12156_SNV_20070510.chr16_19214435fwd/C/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag10/09/0710/14/07129Genomicunknown
ss80547214HGSV|Cor18507_SNV_20070510.chr16_19214435fwd/C/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag11/23/0711/26/07130Genomicunknown
ss90341831BCMHGSC_JDW|JWB-0928854fwd/C/Ggtatgtagggtgccaagtaattttaggacagtgggagtgagaaaagtggtttatcaccag02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs179208|allelePos=837|totalLen=1037|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 TCATTAGTTG CGGGGGCTGT GTCTTAATTT TTGTTCAAGA AAATAGGAAC AGGCTAAGAA
 ATGTGAATGT TTGCTGTGAT GTTTTGTGTT GCTGTGCTGT GGGGTTATTT TACATTTTTG
 GAGTCCTGCC TTCCATCTGG GGcagggttt ctcagtcctg gcactactga catttcgggt
 cggatgattc tttgttgtgg ggagttgttc aatataggat gtttagcagc attcctggcc
 tctacccatt agatgccatt agcaccacca cttccagtgg tgataaccaa aaatgtctcc
 agacattgtc caatgtctcc tggcaagggg cggcgataaa attcccccTC ACTGCTTGag
 agtgatcaac caatttcagt tcgctgggaa ctgtaggagt gcccaggatg tgggactctc
 agggTTttgt tgttgttgtt gttgttttga gtcagggtct tgctctatcg tccaggctgg
 atggagtgca gtggcgtgat catggctcat tgcaatttcg atcttccata ctcaatcgat
 cctcccacct cagagtagct aggactacag gcacactcca ccactctcgg ctaatttttg
 tattttttat agagatgggg ttttaccatg ttgcccagtc tagtcttgaa ctcctggact
 caagcagtcc acccacctca gcctcccaag gtgttggtat tacaggcgtg agccaccaca
 cccagccagg actcttgatt ttaaaactgg gatggtcctg gtcacactgg gatggcttgg
 tcaccctaCT TTCATCTCTA ATATGAGTAT GTAGGGTGCC AAGTAATTTT AGGACA
 S
 GTGGGAGTGA GAAAAGTGGT TTATCACCAG CAAAAACTGA GTCATCCCAG TCACTCCTGG
 ACAAACTTAG CCAAGTTCTC ATGGATGAGT GTCCTTGGTT ACTGAGTGGA AAGAAGGTAG
 AAATGATTTG CTGGTAGAAA TGATTTGCTG CTTCTCATCC ATGCTAAGGG AGAAACTGCT
 GAAAAAGTCG TCCCAGGCAG

  GeneView back to top
GeneView via analysis of contig annotation: LOC728276 hypothetical LOC728276
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->XM_001129496
function
HuRefNW_001838381->XM_001723904
function
CeleraNW_926151->XM_001126977
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010393->XM_001129496->XP_00112949610620013forwardintron
HuRefNW_001838381->XM_001723904->XP_001723956536877forwardintron
CeleraNW_926151->XM_001126977->XP_001126977554942forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs179208 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_001838381.153687717844101plusCalt_assembly_8HuRefHuRefview836
16NW_926151.155494218454807plusCalt_assembly_1CeleraCeleraview836
16NT_010393.151062001319214435plusCref_assemblyreferencereferenceview836

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010393 U91321 U91321.1
dbSNP Blast Analysis
GenBank HTGS Finished:
U91321.1

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/G
G/G
HWPC
G
ss1853278HapMap-CEUEuropean 120IG 0.067 0.933 1.000 0.033 0.967
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 86IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 1.000 1.000
ss24524224AFD_EUR_PANELEuropean 48IG 0.083 0.917 1.000 0.042 0.958
AFD_AFR_PANELAfrican American 46IG 0.043 0.957 1.000 0.022 0.978
AFD_CHN_PANELAsian 48IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.025+/-0.10933226090

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .