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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2280031          
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:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_003471.3:c.1065T>C
NM_172159.3:c.1044T>C
NM_172160.2:c.1098T>C
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 ss76889775 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2280031 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
ss3217945YUSUKE|IMS-JST028029byFreqfwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga09/05/0110/10/03100Genomicunknown
ss23920661PERLEGEN|afd3141615byFreqrev/BC/Ttcctctcctcccagcgtggtgcctgagaaagaaggtgtgagttctgtgctcctgggatca08/10/0409/13/04123Genomicunknown
ss28508569MGC_GENOME_DIFF|BC043166x37550867-T62744372Crev/BC/Ttcctctcctcccagcgtggtgcctgagaaagaaggtgtgagttctgtgctcctgggatca08/25/0408/25/04126cDNAunknown
ss48424335APPLERA_GI|hCV2764248byFreqfwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga09/28/0511/03/06126Genomicunknown
ss66677107ILLUMINA|HumanHap300v1.1_rs2280031fwd/BA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga11/09/0611/09/06127Genomicunknown
ss67241285ILLUMINA|HumanHap550v1.1_rs2280031fwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga11/14/0611/14/06127Genomicunknown
ss67637994ILLUMINA|HumanHap650Yv1.0_rs2280031fwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga11/14/0611/14/06127Genomicunknown
ss68880219PERLEGEN|PGP03141615byFreqrev/BC/Ttcctctcctcccagcgtggtgcctgagaaagaaggtgtgagttctgtgctcctgggatca01/30/0708/14/07127Genomicunknown
ss70719634ILLUMINA|HumanHap550v3.0__rs2280031fwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga04/20/0703/30/08130Genomicunknown
ss71287924ILLUMINA|HumanHap650Yv3.0_rs2280031fwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga04/23/0704/23/07127Genomicunknown
ss75590509ILLUMINA|ILMN_Human_1M_rs2280031fwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga08/28/0708/29/07129Genomicunknown
ss76773508AFFY|AFFY_6_1M_SNP_A-8634761rev/BC/Tcgtggtgcctgagaaagaaggtgtgagttctg08/28/0708/30/07129Genomicunknown
ss76889775SI_EXO|NT_005612.15_62744364rev/BC/Ttcctctcctcccagcgtggtgcctgagaaagaaggtgtgagttctgtgctcctgggatca09/20/0709/20/07129Genomicunknown
ss79125886ILLUMINA|HumanHap300v2.0_rs2280031fwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga04/18/0711/18/07130Genomicunknown
ss84018795KRIBB_YJKIM|KHS603519fwd/TA/Gtgatcccaggagcacagaactcacaccttctttctcaggcaccacgctgggaggagagga12/04/0712/06/07130Genomicunknown
ss105107686PHARMGKB_PAT|PS206269_PA154294348_317rev/BC/Ttcctctcctcccagcgtggtgcctgagaaagaaggtgtgagttctgtgctcctgggatca07/23/0807/23/08130Genomicunknown
ss105110106PHARMGKB_PAT|PS207627_PA156037663_317rev/BC/Ttcctctcctcccagcgtggtgcctgagaaagaaggtgtgagttctgtgctcctgggatca07/23/0807/23/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2280031|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TATGTATATT GTCCTATGAC TTAAATTTCC AAGCAAGTTA TCAGGCCGGC TTTTATGGCG
 AGGCCTGGGA AGTCAGTTGC CACGTATAAC ACTGCAATGC ACTCTTCCAC AGAAACAAAC
 CATCCCAAGA AATGAGCTTT GGGAATACTG CCTGTTCATA GGCAGAGGAC AACCCTGGAT
 CCATGTACTG GGAAAGTGTT CTGTTGCCTT TGTTCCCCCT ACTCTTGCCC CACCCAGGAC
 AGAGAGGGGG AGAGATGGGA CACTGCCTGG AGATAGCCTC AAAGGCACCA TTAAATTCCC
 TGATGTTGGA AGGGGCTGCA GTACTTGCCT GAATGGCACC AAGGTTTTCA ATGAGTTGTT
 CAGGAGTGGA TGATCCCAGG AGCACAGAAC TCACACCTTC
 R
 TTTCTCAGGC ACCACGCTGG GAGGAGAGGA CACTGGGTCA GTTTATCAAA GCACTTCCAA
 TCGTTGATTA GCTTATAAAC ACCTGCTACA GCTGTTTGTT GCAGCCAAAA TTTATTAACT
 TCTTTTTGTG GAGGATGTAC AGTGCTTCCT AGGATTAAAA ACCTGAGCAG CACCCCCTGT
 TGTGTAGAAG ATTTGACAGA ATCTGTCAAA GCCCAGCTGG GAGGGGAAAT GCAAATGCAT
 AGAGGCGCTG GACAATGGAT TGTAAGATTC TCTCCAGCAC GCTCAGCTGC CCTCAAGTAG
 AAGCAGAAAA CACAGATGCA CTGCTGTCTT TCTTGCTTCT CCGCTGGTTT TCCAATTGCT
 AGCCTACTAT ATGTCTCTTA ATTAACACTC AATGCATTTG

  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_005612.15 BC043166
dbSNP Blast Analysis
UniGene Cluster ID
157818
3D structure mapping
NP_003462  NP_751891  NP_751892  

  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
ss105107686 PA154294349 292 AF 0.753 0.247
ss105110106 PA156037664 26 AF 0.692 0.308
ss23920661 AFD_EUR_PANEL European 48 IG 0.583 0.417 0.200 0.792 0.208
AFD_AFR_PANEL African American 46 IG 0.478 0.478 0.043 0.403 0.717 0.283
AFD_CHN_PANEL Asian 48 IG 0.417 0.583 0.050 0.708 0.292
CHMJ Asian 74 IG 0.730 0.270
ss3217945 JBIC-allele 1484 AF 0.744 0.256
ss48424335 HapMap-CEU European 120 IG 0.667 0.267 0.067 0.200 0.800 0.200
HapMap-HCB Asian 90 IG 0.444 0.422 0.133 0.752 0.656 0.344
HapMap-JPT Asian 88 IG 0.455 0.477 0.068 0.439 0.693 0.307
HapMap-YRI Sub-Saharan African 120 IG 0.633 0.350 0.017 0.317 0.808 0.192
AGI_ASP population multiple 56 IG 0.786 0.214 0.527 0.893 0.107
ss68880219 HapMap-CEU European 120 GF 0.667 0.267 0.067 0.800 0.200
HapMap-HCB Asian 90 GF 0.444 0.422 0.133 0.656 0.344
HapMap-JPT Asian 90 GF 0.467 0.467 0.067 0.700 0.300
HapMap-YRI Sub-Saharan African 120 GF 0.633 0.350 0.017 0.808 0.192

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.369+/-0.220 1302 1091 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
byClusterbyFreqbySubmitterwithHapMapFreq
Validated by: PERLEGEN
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .