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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs7779          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:52/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_016002.2:c.1252G>C
NP_057086.2:p.Gly418Arg
NT_004836.17:g.11688353G>C
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 ss109132126 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7779 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
ss9699CGAP-GAI|50563fwd/TC/Gcagagctgctaataacactaaactcaatacgtgtttgttgagtctgtcaatcaactttgt08/23/9910/10/0352cDNA99 %
ss1511066LEE|55612byFreqrev/BC/Gacaaagttgattgacagactcaacaaacacgtattgagtttagtgttattagcagctctg09/13/0005/16/0498cDNAunknown
ss4404751LEE|e55612rev/BC/Gacaaagttgattgacagactcaacaaacacgtattgagtttagtgttattagcagctctg04/26/0210/10/03106cDNAunknown
ss16223977CGAP-GAI|1455377fwd/TC/Gcagagctgctaataacactaaactcaatacgtgtttgttgagtctgtcaatcaactttgt11/18/0311/22/03120cDNAunknown
ss66437259AFFY|SNP_A-2181401byFreqrev/BC/Gcagactcaacaaacacgtattgagtttagtgt10/29/0608/14/07127Genomicunknown
ss68800437PERLEGEN|PGP04769069byFreqrev/C/Gacaaagttgattgacagactcaacaaacacgtattgagtttagtgttattagcagctctg01/30/0708/14/07127Genomicunknown
ss76215470AFFY|AFFY_6_1M_SNP_A-2181401rev/C/Gcagactcaacaaacacgtattgagtttagtgt08/28/0708/30/07129Genomicunknown
ss81404284KRIBB_YJKIM|KHS30469fwd/C/Gcagagctgctaataacactaaactcaatacgtgtttgttgagtctgtcaatcaactttgt11/30/0711/30/07130Genomicunknown
ss1091321261000GENOMES|CEU.trio.12.15.2008_292356_chr1_244997187rev/C/Gacaaagttgattgacagactcaacaaacacgtattgagtttagtgttattagcagctctg12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs7779|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 TAGGGTAAGC TAGGACAATT TCCTACTTTT TAATATATAG ATATTTTAGA TTTGACAATC
 GTTTCCACAT ACACTCAGAC AGGCTTACAG AAGAATTTCA AATATCAAAT AGAGAAGCTG
 TTAATTCACG CACGTTATGA CTTCAGTTAA TTCTTCCAGT GTTTAGACTT CAGAGCTGCT
 AATAACACTA AACTCAATAC
 S
 GTGTTTGTTG AGTCTGTCAA TCAACTTTGT TTTGGAAAAA GCTGCTCCAG GTGTGAAGAC
 CCCGCCCCTA TAAAACAATA ACAAGAGAAA ACAGTGCACT CAGCTCCTCT CCAGTCTCCT
 ATTTCACAGG CCTCACTATC AAATTGCTAC AGAACCCCTG AAAACCCAAG TCTTCATGGT
 AATCACGGCT ACCTTTGATT

  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
NC_000001.8 AA429301 AI126957 Hs.238126
dbSNP Blast Analysis
UniGene Cluster ID
498397

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 G/G
 HWP C
 G
ss1511066 CEPH 184 AF 0.910 0.090
HapMap-CEU European 120 IG 0.850 0.150 0.584 0.925 0.075
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 1.000 1.000
EURAME 30 GF 0.933 0.067 1.000 0.967 0.033
AFRAME 28 GF 1.000 1.000
ss66437259 HapMap-CEU European 118 GF 0.847 0.153 0.924 0.076
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000
ss68800437 HapMap-CEU European 120 IG 0.850 0.150 0.925 0.075
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 1.000 1.000
ss76215470 ICMHP 4 IG 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.042+/-0.138 1126 917 270 0

  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 UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .