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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2298719          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
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_001128588.1:c.667A>G
NM_015865.2:c.499A>G
NM_015865.3:c.499A>G
NP_001122060.1:p.Met223Val
NP_056949.1:p.Met167Val
NP_056949.2:p.Met167Val
NT_010966.13:g.24805551A>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 ss28501769 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2298719 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
ss3243729YUSUKE|IMS-JST053814byFreqfwd/BC/Ttgaagacggggaggtcccatttgctgagcaggaattcaatgcacttgagaaaattgggct09/05/0110/10/03100Genomicunknown
ss24037161PERLEGEN|afd4230174byFreqrev/TA/Gagcccaattttctcaagtgcattgaattcctgctcagcaaatgggacctccccgtcttca08/10/0409/13/04123Genomicunknown
ss28501769IMCJ-GDT|IMCJ-SLC14A1_10-AGbyFreqrev/TA/Gagcccaattttctcaagtgcattgaattcctgctcagcaaatgggacctccccgtcttca08/20/0411/02/06126Genomicunknown
ss28509992MGC_GENOME_DIFF|BC050539x29823167-A24805551Grev/TA/Gagcccaattttctcaagtgcattgaattcctgctcagcaaatgggacctccccgtcttca08/25/0408/25/04126cDNAunknown
ss65726740ILLUMINA|Human1-rs2298719fwd/BC/Ttgaagacggggaggtcccatttgctgagcaggaattcaatgcacttgagaaaattgggct10/10/0610/10/06127Genomicunknown
ss69213285PERLEGEN|PGP04230174byFreqrev/TA/Gagcccaattttctcaagtgcattgaattcctgctcagcaaatgggacctccccgtcttca01/30/0708/14/07127Genomicunknown
ss74863492ILLUMINA|ILMN_Human_1M_rs2298719fwd/BC/Ttgaagacggggaggtcccatttgctgagcaggaattcaatgcacttgagaaaattgggct08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2298719|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 GAGCCAGGGC GAATGTGAGA AGCCAGTGTC TCTTACCTCC AGGGCACTGA GGTCAGACCA
 GGAGATATTT GGAGCTGTAG TTATAGGTAT GACCAGTTTG GCTGGAAAGA ATGGATTGTA
 ATGTCCTGTG GCTGAAAGGT ACATTGACAA CGCCATGTTG AAAGGGAGGG TGAAGACGGG
 GAGGTCCCAT TTGCTGAGCA
 Y
 GGAATTCAAT GCACTTGAGA AAATTGGGCT AAAAAAAGAA CAGAGCAAAA GAATGTGCAT
 GTGACAAAGC AGGCTGACAC ACGGAATCGC TATACTCTGG AGGGGCTTTG TTTCACCTGC
 CAACAGGCCC CTTACGTGTT GTGTTGGCAC ATTTGCCACA GAAAGAAAAC TTGGGATAAA
 TCCTATTATA GAGGCAGTAA

  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_000018.8 BC050539
dbSNP Blast Analysis
UniGene Cluster ID
101307

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss24037161 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 44 IG 1.000 1.000
AFD_CHN_PANEL Asian 48 IG 0.042 0.417 0.542 0.655 0.250 0.750
ss28501769 HapMap-CEU European 118 IG 1.000 1.000
HapMap-HCB Asian 90 IG 0.044 0.267 0.689 0.584 0.178 0.822
HapMap-JPT Asian 88 IG 0.045 0.250 0.705 0.479 0.170 0.830
HapMap-YRI Sub-Saharan African 120 IG 1.000 1.000
ss3243729 JBIC-allele 1486 AF 0.157 0.843
ss69213285 HapMap-CEU European 120 GF 1.000 1.000
HapMap-HCB Asian 90 GF 0.044 0.267 0.689 0.178 0.822
HapMap-JPT Asian 90 GF 0.044 0.244 0.711 0.167 0.833
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.140+/-0.225 666 544 276 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 .