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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2267161          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_004861.1:c.85G>A
NP_004852.1:p.Val29Met
NT_011520.11:g.10343864C>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 ss76896511 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2267161 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
ss3200412YUSUKE|IMS-JST020496byFreqfwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc09/05/0110/10/03100Genomicunknown
ss5604143RIKENSNPRC|ssj0002899rev/TA/Gggcgcgctcttcactagtttcctgctgctgtgtactcctatgccgtgcccccgctgcatg10/18/0210/10/03110Genomicunknown
ss11007280BCM_SSAHASNP|chr22.NT_011520.9_10343864fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc06/30/0310/25/06116Genomicunknown
ss13348211SC_SNP|NT_011520.9_10343864fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc10/22/0310/31/03119Genomicunknown
ss16248255CGAP-GAI|1494775rev/TA/Gggcgcgctcttcactagtttcctgctgctgtgtactcctatgccgtgcccccgctgcatg11/18/0311/22/03120cDNAunknown
ss28497815MGC_GENOME_DIFF|29807292-C10343864Tfwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc08/20/0408/20/04126cDNAunknown
ss28510893MGC_GENOME_DIFF|BC019077x29807292-C10343864Tfwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc08/25/0408/25/04126cDNAunknown
ss28512604MGC_GENOME_DIFF|BC014649x29807292-C10343864Tfwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc08/25/0408/25/04126cDNAunknown
ss48402681APPLERA_GI|hCV2629047byFreqfwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc09/28/0511/03/06126Genomicunknown
ss65731060ILLUMINA|Human1-rs2267161fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc10/10/0610/10/06127Genomicunknown
ss65827703KRIBB_YJKIM|KHS3492byFreqfwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc10/17/0612/16/06127Genomicunknown
ss66612296ILLUMINA|HumanHap300v1.1_rs2267161fwd/TC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc11/09/0611/09/06127Genomicunknown
ss67239220ILLUMINA|HumanHap550v1.1_rs2267161fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc11/14/0611/14/06127Genomicunknown
ss67635765ILLUMINA|HumanHap650Yv1.0_rs2267161fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc11/14/0611/14/06127Genomicunknown
ss68405787CSHL-HAPMAP|sanger:assay:4242900:1byFreqfwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc01/11/0701/16/07127NAunknown
ss69274506PERLEGEN|PGP00121599fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc01/30/0701/30/07127Genomicunknown
ss70717557ILLUMINA|HumanHap550v3.0__rs2267161rev/TA/Gggcgcgctcttcactagtttcctgctgctgtgtactcctatgccgtgcccccgctgcatg04/20/0703/30/08130Genomicunknown
ss71285683ILLUMINA|HumanHap650Yv3.0_rs2267161fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc04/23/0704/23/07127Genomicunknown
ss75482639ILLUMINA|ILMN_Human_1M_rs2267161fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc08/28/0708/29/07129Genomicunknown
ss76584547AFFY|AFFY_6_1M_SNP_A-8445823fwd/BC/Tacggcataggagtacacagcagcaggaaacta08/28/0708/30/07129Genomicunknown
ss76896511SI_EXO|NT_011520.11_10343864fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc09/20/0709/20/07129Genomicunknown
ss79124316ILLUMINA|HumanHap300v2.0_rs2267161fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc04/18/0711/18/07130Genomicunknown
ss84012622KRIBB_YJKIM|KHS601577fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc12/04/0712/06/07130Genomicunknown
ss85542084HGSV|Cor18517_SNV_20070510.chr22_29277849fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc12/06/0712/09/07130Genomicunknown
ss96121725HUMANGENOME_JCVI|1103691028489fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc03/25/0803/25/08130Genomicunknown
ss1126079211000GENOMES|CEU.trio.12.15.2008_3799404_chr22_29283295fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc12/15/0812/17/08130Genomicunknown
ss1141388761000GENOMES|NA19240_2008_12_16_3434818_chr22_29283295fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc12/18/0812/18/08130Genomicunknown
ss117388599ILLUMINA-UK|NA18507_000017048_NCBI36.1_chr22_29283295fwd/BC/Tcatgcagcgggggcacggcataggagtacacagcagcaggaaactagtgaagagcgcgcc01/19/0901/19/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2267161|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TATTTTTAGT AGAGATGGGG TTTCACCATG TTGGCCAGGC TGGTCTCGAA CTCCTGACCT
 CAGACGATCT GCCCGCCTGG GCCTCCCAAA GTGCTAGGAT TACAGGCGTG AGTTGCCGTG
 CCCAGCCGAA AGGCTCTGTT TTTATCCCCA CTTCACAGAT GGGCACACCA AGGCTCAGAG
 TTACACGGCG AGCTCTGCCA TCAGTGGAAT TTCTGTCTGG CACAGCATGG TGCAGGGTGC
 AGGGTGGCTA CCCAAGATCA CTGGGGCAGG CCCTGTGGTA ATTACAGGGC CCCATGGGTG
 GGGTGCCATC CCTCCCCCAC CTACACCCAT CATCTGCCCA GCTGGGCCAC TCACGTGGAG
 GCCAGGCCGG CATGCAGCGG GGGCACGGCA TAGGAGTACA
 Y
 CAGCAGCAGG AAACTAGTGA AGAGCGCGCC CAGCACCAGC CCCTTAGCCA TGGACTCCCA
 GGGCTTCTTC TGCGGTGGCA GCATCTCAGA CACCTGCAGG GGCAGCACAG AGTAGGGCAA
 GTGTCAGGAA GCTGGCCCCA GGGAGCCCCC AAGGCTGCCC AGGCCTGGCA GTTGAGCCCT
 GCCTTTGCCT GCTCTGTGGC CCCCCAGCAG GGTCCAGACA GGGACAGAGA GGCACTGGAG
 AGATAGACTG ACAACCACCT GGAAAGAGAC AGCCCCAGGG TTGCAGAGAC GGTGGGTGAA
 GCAACTCAAA GAGAGGTTGG GGAATGGGGC AGGGAGAAGG TTAAAATTTA AAAATTAAAA
 TGAACCGGGT AGAGAACCAG GGCCCCAAAC TTTCCACTCC

  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_011520.11 ABBA01055300 BC014649 BC019077 BM923857
dbSNP Blast Analysis
UniGene Cluster ID
17958

  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
ss3200412 JBIC-allele 1310 AF 0.663 0.337
ss48402681 HapMap-CEU European 120 IG 0.350 0.550 0.100 0.200 0.625 0.375
HapMap-HCB Asian 90 IG 0.489 0.378 0.133 0.371 0.678 0.322
HapMap-JPT Asian 88 IG 0.318 0.500 0.182 1.000 0.568 0.432
HapMap-YRI Sub-Saharan African 120 IG 0.283 0.550 0.167 0.403 0.558 0.442
ss65827703 KHP1 180 AF 0.367 0.511 0.122 0.439 0.622 0.378

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict		 Additional Freq. Data
0.476+/-0.108 1208 1002 0 0 ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .