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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs17306779          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_001818.2:c.105A>G
NT_077567.3:g.5182164A>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 ss61714551 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17306779 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
ss24535498PERLEGEN|afd2201741byFreqfwd/TA/Ggctccttcaggttccgaggaacagagctgtgaggtcaccaaattagcaatagaagctggc08/10/0409/13/04123Genomicunknown
ss61714551SI_EXO|NT_077567.3_5182164byFreqfwd/TA/Ggctccttcaggttccgaggaacagagctgtgaggtcaccaaattagcaatagaagctggc07/11/0603/31/08127Genomicunknown
ss76666891AFFY|AFFY_6_1M_SNP_A-8528165rev/BC/Tctaatttggtgacctcacagctctgttcctcg08/28/0708/30/07129Genomicunknown
ss78324857HGSV|Cor12878_SNV_20070510.chr10_5232164fwd/TA/Ggctccttcaggttccgaggaacagagctgtgaggtcaccaaattagcaatagaagctggc10/17/0710/18/07129Genomicunknown
ss86242339CORNELL|hCV25472375fwd/TA/Ggctccttcaggttccgaggaacagagctgtgaggtcaccaaattagcaatagaagctggc01/21/0801/21/08129Genomicunknown
ss88076964BCMHGSC_JDW|JWB-0227820fwd/TA/Ggctccttcaggttccgaggaacagagctgtgaggtcaccaaattagcaatagaagctggc02/26/0802/27/08129Genomicunknown
ss105099503KRIBB_YJKIM|KHS1491826fwd/TA/Ggctccttcaggttccgaggaacagagctgtgaggtcaccaaattagcaatagaagctggc07/10/0807/11/08130Genomicunknown
ss1091876621000GENOMES|CEU.trio.12.15.2008_2283831_chr10_5232164fwd/TA/Ggctccttcaggttccgaggaacagagctgtgaggtcaccaaattagcaatagaagctggc12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17306779|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 CGATCCTTCC GGTAAACCAA AGCAAGAACT CAGGATACAG AAAGCCCTCT GTCCTTGCCA
 TAAGGTAGAG GGTCTAATTG AGCTGGTTAA CACAAGCCTG TAGATGGCAA AACTTAAAGA
 ACAAAACTAA AAGAGCACCC TGTAACACAT GCCCACTGGG GCTTCAGGAG CTGTAAACAT
 CCACACCTAG ACACTGTCAA CGGGTCATAG TCCCACAACC TGCCCCCATC TGTATGCTCC
 CCTAGAGGTC TGAGCAGCGG GGGCCTGAAG AAGCGAGCCA CACCCCCACT GCACACCCTG
 TGAGGACAAG GGAACTTTTC CTGTTTCACT ACCTCTCAAG CACATTGATC ACCAAATACT
 ACCTTTCGTT GCTCCTTCAG GTTCCGAGGA ACAGAGCTGT
 R
 GAGGTCACCA AATTAGCAAT AGAAGCTGGC TTCCGCCATA TTGATTCTGC TTATTTATAC
 AATAATGAGG AGCAGGTTGG ACTGGCCATC CGAAGCAAGA TTGCAGATGG CAGTGTGAAG
 AGAGAAGACA TATTCTACAC TTCAAAGGTA CTGTGCCTAT GATGAGCATG TATGCACATG
 TGTTTAATGG GATTGTGTGG AGATGACAAT TCTGTAACTG GTTCAGTAGT TGTGGGTGAA
 TTGTGCTTAT TAGTTCCAAT TTATTCACAC ATATTCAGGT ATTAAAGCTA AAATAAAAGG
 CAGAGAATGA TGATGCCTTT CTCATCATTG TTGTGTTCAA ATTTACTACT TGAAAGTTAC
 TTTAGGTTTT GAGCCTCAGC TCAGATCAGT ATAATTATTT

  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
NT_077567.3
dbSNP Blast Analysis
UniGene Cluster ID
498514
3D structure mapping
NP_001809  

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss24535498 AFD_EUR_PANEL European 48 IG 0.542 0.417 0.042 0.655 0.750 0.250
AFD_AFR_PANEL African American 46 IG 0.739 0.261 0.479 0.870 0.130
AFD_CHN_PANEL Asian 48 IG 0.625 0.333 0.042 1.000 0.792 0.208
ss61714551 HapMap-CEU European 120 IG 0.600 0.267 0.133 0.733 0.267
HapMap-HCB Asian 90 IG 0.689 0.289 0.022 0.833 0.167
HapMap-JPT Asian 90 IG 0.911 0.089 0.956 0.044
HapMap-YRI Sub-Saharan African 120 IG 0.867 0.133 0.933 0.067

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.262+/-0.250 1263 1052 15 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 .