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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2230491          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_004857.3:c.299C>T
NP_004848.3:p.Pro100Leu
NT_026437.11:g.45935164C>T
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 ss48402356 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2230491 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
ss3177626WICVAR|WI-21818byFreqfwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa06/28/0104/07/0498cDNAunknown
ss48402356APPLERA_GI|hCV15852884byFreqfwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa09/28/0511/03/06126Genomicunknown
ss66836084ILLUMINA|HumanHap300v1.1_rs2230491fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa11/09/0611/09/06127Genomicunknown
ss67235610ILLUMINA|HumanHap550v1.1_rs2230491fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa11/14/0611/14/06127Genomicunknown
ss67631720ILLUMINA|HumanHap650Yv1.0_rs2230491fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa11/14/0611/14/06127Genomicunknown
ss69160033PERLEGEN|PGP04241310byFreqfwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa01/30/0708/14/07127Genomicunknown
ss70713944ILLUMINA|HumanHap550v3.0__rs2230491rev/TA/Gtttattgcaggttgcatttcaccctccaatgcttttgctgctttgaagactctgaccttt04/20/0703/30/08130Genomicunknown
ss71281638ILLUMINA|HumanHap650Yv3.0_rs2230491fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa04/23/0704/23/07127Genomicunknown
ss74809053AFFY|SNP_M-181481fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa08/09/0708/09/07128Genomicunknown
ss75905372ILLUMINA|ILMN_Human_1M_rs2230491fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa08/28/0708/29/07129Genomicunknown
ss79121757ILLUMINA|HumanHap300v2.0_rs2230491fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa04/18/0711/18/07130Genomicunknown
ss84001977KRIBB_YJKIM|KHS598251fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa12/04/0712/06/07130Genomicunknown
ss86348386CANCER-GENOME|12183fwd/BC/Taaaggtcagagtcttcaaagcagcaaaagcattggagggtgaaatgcaacctgcaataaa01/25/0801/25/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2230491|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 AAATGGAAAC CACAATTTCA GAAATTCATG TAGAAAACAA GGATGAGAAG AGATCAGCAG
 AAGGTAGTCC TGGGGCTGAA AGGCAGAAGG AAAAGGCATC CATGCTTTGC TTCAAGAGAA
 GAAAGAAAGC AGCCAAAGCA CTGAAGCCCA AAGCTGGCTC TGAAGCTGCT GATGTGGCAA
 GGAAGTGTCC ACAAGAAGCA GGAGCTTCTG ATCAGCCAGA GCCCACACGG GGGGCCTGGG
 CCTCACTCAA ACGTCTTGTA ACACGCAGGA AAAGGTCAGA GTCTTCAAAG CAGCAAAAGC
 Y
 ATTGGAGGGT GAAATGCAAC CTGCAATAAA TGCTGAGGAT GCTGATCTTT CTAAGAAAAA
 GGCAAAATCT AGACTTAAGA TTCCCTGCAT AAAATTCCCA AGAGGGCCAA AAAGGAGTAA
 TCATTCCAAA ATTATAGAAG ACTCAGACTG CAGCATCAAA GTCCAGGAAG AAGCTGAAAT
 TTTGGATATA CAAACACAGA CCCCATTGAA TGATCAGGCA ACAAAGGCTA AGTCAACCCA
 GGATCTAAGT GAAGGCATCT CACGGAAAGA TGGTGATGAG GTCTGTGAAT CAAATGTGAG

  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
NM_004857
dbSNP Blast Analysis
UniGene Cluster ID
532489

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 HWP C
 T
ss3177626 MITOGPOP6 multiple 62 IG 0.903 0.097 1.000 0.952 0.048
ss48402356 HapMap-CEU European 120 IG 0.767 0.233 0.317 0.883 0.117
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
AGI_ASP population multiple 56 IG 0.857 0.143 0.752 0.929 0.071
ss69160033 HapMap-CEU European 120 GF 0.767 0.233 0.883 0.117
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 0.983 0.017 0.992 0.008
Concordant Genotype Total Sample C/C C/T
ss3177626 31 28 3
ss48402356 1151 901 121
ss69160033 269 247 21
RefSNP Genotype Summary Total Individual C/C C/T
rs2230491 1173 940 123
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5134 ss48402356 C/C CSHL-HAPMAP HapMap-YRI NA19127 YOR077.02 r27_ch14_YRI_illumina:human_1m_beadchip
5134 ss69160033 C/T CSHL-HAPMAP HapMap-YRI NA19127 YOR077.02 chr14-HapMap-YRI
Genotype data submitted for1183 samples from1173 individualsIndividual with multiple genotypes submission:278

  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 YES YES

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Revised: May 25, 2006 1:38 PM .