Skip to main content
NCBI
 dbSNP
PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
transparent GIF
Spacer gif
BUILD 130
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs10462020          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_016831.1:c.1916T>G
NP_058515.1:p.Val639Gly
NT_021937.18:g.2418050T>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 ss76896671 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10462020 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
ss14811422PGP|Per3-21byFreqfwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc11/12/0304/07/04119Genomicunknown
ss48419668APPLERA_GI|hCV25956444byFreqfwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc09/28/0511/03/06126Genomicunknown
ss65724663ILLUMINA|Human1-rs10462020fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc10/10/0610/10/06127Genomicunknown
ss66569855ILLUMINA|HumanHap300v1.1_rs10462020fwd/TG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc11/09/0611/09/06127Genomicunknown
ss66884031ILLUMINA|HumanHap550v1.1_rs10462020fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc11/14/0611/14/06127Genomicunknown
ss66979258ILLUMINA|HumanHap650Yv1.0_rs10462020fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc11/14/0611/14/06127Genomicunknown
ss68757960PERLEGEN|PGP04754354byFreqfwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc01/30/0703/31/08127Genomicunknown
ss70366144ILLUMINA|HumanHap300v2.0_rs10462020fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc04/18/0711/17/07127Genomicunknown
ss70479781ILLUMINA|HumanHap550v3.0__rs10462020rev/TA/Cgcgagtgtggtacctgtctctgggggtgggcatggacaatggtgctgctgtaaccgcatt04/20/0703/30/08130Genomicunknown
ss71003307ILLUMINA|HumanHap650Yv3.0_rs10462020fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc04/23/0704/23/07127Genomicunknown
ss74960133ILLUMINA|ILMN_Human_1M_rs10462020fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc08/28/0708/29/07129Genomicunknown
ss76896671SI_EXO|NT_021937.18_2418050fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc09/20/0709/20/07129Genomicunknown
ss84940500KRIBB_YJKIM|KHS854529fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc12/04/0712/08/07130Genomicunknown
ss87202203BCMHGSC_JDW|JWB-0007541fwd/BG/Taatgcggttacagcagcaccattgtccatgcccacccccagagacaggtaccacactcgc02/26/0802/26/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10462020|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 TGTCCAAGCC TTACAAGGTA ACAAGAATGC CCCTCAGAGT TAAATTCAAA GAACTGTAAA
 TACATCCTTC TTGTTTCTCT TTAATGTCTT ATATTGTTAT AAGCATAAAA TTCTGGTTTC
 ATATTACCTC TTTATGACAG TAAGGTTTAA TTTCTCAGTT ACAAACTTCT GTAAACTGGG
 TCTTTTATGT AAATTTCTCG TTGGGAATTT TTCTTTTCAC TGTCAGTTTC TCTTACACCA
 CCAGCTGGTT TGCAAATCCC AGCCATACCT AAATCAGAAA TGCCAACAAA TGGACGGTCC
 ATAGACACAG GAGGAGGAGC TCCACAGATC CTGTCCACGG CGATGCTGAG CTTGGGGTCG
 GGCATAAGCC AATGCGGTTA CAGCAGCACC ATTGTCCATG
 K
 CCCACCCCCA GAGACAGGTA CCACACTCGC CTCTTACTTT GAAAATATAC TCAACTTTAA
 CTACATTGTG ATGAGAAAAC AAAAGTCATG AATACCATTC GCTCGGTTGT AACTTCTAAA
 CTACACATAT TTTTTCCTTT CTTTAGTTCA GTTAAAGTAT TTCTGGAAAC ATTATCATGT
 TTATGTTGGT TACATATTTT GGACAGTATT TCTCAGTTAT GTTATTTGTC AATGAAATCA
 GTTGACACAT ATAAAGCACT TAATACAGTA CCTAGTAGGT AGGTATTAGC CCTCAATTAG
 TGTTAGCCAT TATTAATGCA ATTATTGATG GCACTGTGTT AGGTTACTTC CTTGCTGACT
 TTCACAGAAT GTGTTCCTTT CACCTGCATT TCACCATCCT

  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_028054.9
dbSNP Blast Analysis
UniGene Cluster ID
533339

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source G/G
 G/T
 T/T
 HWP G
 T
ss14811422 PGP-Caucasian 182 AF 0.170 0.830
ss48419668 HapMap-CEU European 120 IG 0.017 0.250 0.733 0.142 0.858
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 90 IG 0.044 0.956 0.022 0.978
HapMap-YRI Sub-Saharan African 118 IG 0.102 0.898 0.051 0.949
AGI_ASP population multiple 70 IG 0.086 0.914 1.000 0.043 0.957
ss68757960 HapMap-CEU European 120 GF 0.267 0.733 0.133 0.867
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 0.022 0.978 0.011 0.989
HapMap-YRI Sub-Saharan African 120 GF 0.067 0.933 0.033 0.967
Concordant Genotype Total Sample G/G G/T T/T
ss48419668 38 3 32
ss76896671 1117 12 210 818
RefSNP Genotype Summary Total Individual G/G G/T T/T
rs10462020 1160 12 213 850
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
161 ss76896671 G/T CSHL-HAPMAP HapMap-CEU NA07029 CEPH1340.01 r27_ch1_CEU_illumina:human_1m_beadchip
225 ss76896671 N/N CSHL-HAPMAP HapMap-CEU NA12043 CEPH1346.11 r27_ch1_CEU_illumina:human_1m_beadchip
5223 ss76896671 G/T CSHL-HAPMAP HapMap-JPT NA18971 JA18971 r27_ch1_JPT_illumina:human_1m_beadchip
5237 ss76896671 G/T CSHL-HAPMAP HapMap-YRI NA18501 YOR004.03 r27_ch1_YRI_illumina:human_1m_beadchip
5240 ss76896671 G/T CSHL-HAPMAP HapMap-YRI NA18504 YOR005.03 r27_ch1_YRI_illumina:human_1m_beadchip
Genotype data submitted for1160 samples from1160 individualsIndividual with multiple genotypes submission: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

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
HAPLOTYPE:Submission | Specifications | Sample HapSet | Sample Individual
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement

Revised: May 25, 2006 1:38 PM .