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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2230193          
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:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_001040280.1:c.542G>A
NM_004233.3:c.545G>A
NP_001035370.1:p.Arg181Gln
NP_004224.1:p.Arg182Gln
NT_007592.14:g.4993645G>A
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 ss48427586 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2230193 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
ss3177306WICVAR|WI-18305byFreqfwd/TA/Gtcccagatttttctaaagctggcatggaacagcttttctcccagttacctccccaaataa06/28/0108/14/0798cDNAunknown
ss23299861PERLEGEN|afd0265701byFreqfwd/TA/Gtcccagatttttctaaagctggcatggaacagcttttctcccagttacctccccaaataa08/10/0409/13/04130Genomicunknown
ss48427586APPLERA_GI|hCV15852164byFreqfwd/TA/Gtcccagatttttctaaagctggcatggaacagcttttctcccagttacctccccaaataa09/28/0511/03/06130Genomicunknown
ss68965976PERLEGEN|PGP00265701byFreqfwd/TA/Gtcccagatttttctaaagctggcatggaacagcttttctcccagttacctccccaaataa01/30/0703/31/08130Genomicunknown
ss74818211AFFY|SNP_M-317324fwd/TA/Gtcccagatttttctaaagctggcatggaacagcttttctcccagttacctccccaaataa08/09/0708/09/07130Genomicunknown
ss74905261ILLUMINA|ILMN_Human_1M_rs16874698fwd/TA/Gtcccagatttttctaaagctggcatggaacagcttttctcccagttacctccccaaataa08/28/0708/29/07129Genomicunknown
ss76486934AFFY|AFFY_6_1M_SNP_A-8348079fwd/TA/Gaaagctggcatggaacagcttttctcccagtt08/28/0708/30/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2230193|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 CTTTCCATAC AGAGACCTAA CAGTAGGGGG TCGAAATGGC CACAATCAGT GAATCTCCTG
 GTCCAAGTTT AGAGACGCCA GTGAAATGGT TGGTACAAAT CCCTTGTGGA GCGAGTGAGG
 CAGTGAGTAT GAGAGCTTCC AGAATGGGTT GTCTAGCCAG CTCTTAGTGA ATAGAGTTTA
 AAAGGAGGTG ACAACTGCTG AATTTTTCCA ATTATTCACT TCACATTTCT TTCATTTCTT
 TTTAGAAGTT TGCACGGCTA CAGAGTATCT TCCCAGATTT TTCTAAAGCT GGCATGGAAC
 R
 AGCTTTTCTC CCAGTTACCT CCCCAAATAA GCATTTAGGG CTAGTGACTC CTCACAAGAC
 AGAACTGGTA TGAGCAGGAT TTCTGCAGGT TCTTCTTCCT GAAGCTGAGG CTCAGGGGTG
 TGCCTGTCTG TTACACTGGA GGAGAGAAGA ATGAGCCTAC GCTGAAGATG GCATCCTGTG
 AAGTCCTTCA CCTCACTGAA AACATCTGGA AGGGGATCCC ACCCCATTTT CTGTGGGCAG
 GCCTCGAAAA CCATCACATG ACCACATAGC ATGAGGCCAC TGCTGCTTCT CCATGGCCAC

  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_004233
dbSNP Blast Analysis
UniGene Cluster ID
484703

  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
ss23299861 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.261 0.739 0.479 0.130 0.870
AFD_CHN_PANEL Asian 48 IG 1.000 1.000
ss3177306 MITOGPOP6 multiple 46 IG 0.043 0.957 1.000 0.022 0.978
HapMap-CEU European 120 IG 1.000
HapMap-HCB Asian 90 IG 1.000
HapMap-JPT Asian 88 IG 1.000
HapMap-YRI Sub-Saharan African 118 IG 0.085 0.915
ss48427586 HapMap-CEU European 118 IG 1.000 1.000
HapMap-HCB Asian 88 IG 1.000 1.000
HapMap-JPT Asian 90 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.017 0.150 0.833 0.092 0.908
AGI_ASP population multiple 68 IG 0.088 0.912 1.000 0.044 0.956
ss68965976 HapMap-CEU European 120 GF 1.000 1.000
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 0.017 0.150 0.833 0.092 0.908

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.057+/-0.159 1050 839 283 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreq UNKNOWN YES YES

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Revised: May 25, 2006 1:38 PM .