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: rs10401800          
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:C/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_014475.3:c.4G>C
NP_055290.1:p.Ala2Pro
NT_011109.15:g.21705172G>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 ss14691157 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10401800 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
ss14691157BCM_SSAHASNP|chr19.NT_011109.15_21705172byFreqfwd/TC/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc11/10/0310/25/06119Genomicunknown
ss17612262CSHL-HAPMAP|CSHL-HuCC-200402.chr19.NT_011109.15_21705172fwd/TC/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc02/19/0403/04/04120Genomicunknown
ss23812946PERLEGEN|afd1615171byFreqfwd/TC/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc08/10/0409/13/04123Genomicunknown
ss44167520ABI|hCV3170896fwd/C/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc07/18/0507/18/05126Genomicunknown
ss48404983APPLERA_GI|hCV3170896byFreqfwd/C/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc09/28/0511/03/06126Genomicunknown
ss65730298ILLUMINA|Human1-rs10401800fwd/?C/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc10/10/0610/10/06127Genomicunknown
ss69229883PERLEGEN|PGP01615171byFreqfwd/C/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc01/30/0703/31/08127Genomicunknown
ss1152249801000GENOMES|NA19240_2008_12_16_3270747_chr19_54128794fwd/C/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc12/18/0812/19/08130Genomicunknown
ss117725822ILLUMINA-UK|NA18507_000055285_NCBI36.1_chr19_54128794fwd/C/Gaggtgccgagggctccgcatcgcaaccatgcgctgcgctggggcatcgtgtctgtcggcc01/19/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10401800|allelePos=201|totalLen=701|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 AAGGCGGAGC TAAACGGTGC ATTCGCCCAG CGGGGAAGCT AGAACTAAAT GACCGCTCTG
 CCGACTGGAG CCAACGAGAA TCGGCGTAGG CGCAATACGG GCGGAGGATG GGGACCCGCC
 CCCGGGGTGG GCGGGGCGTC AGGTACTTAA TTCGCGCCTG GAGGGACCGA AGGTGCCGAG
 GGCTCCGCAT CGCAACCATG
 S
 CGCTGCGCTG GGGCATCGTG TCTGTCGGCC TCATCTCCAG CGACTTCACA GCCGTGCTGC
 AGACGCTGCC TCGCTCTGAG CACCAGGTCT GCCCGCCCTC CGGATTCTGG GGAAGAGGAG
 GCGGGGGGCG GGACTCCAGA GTCTAAAGGA GGAGGGAGTT TAGGGTTCAG GACTAGTGAG
 TGGGTCGTCA TTGCAGTGAA ACGTCTGTTT CCTTGCTACC TCCTTCTCCA TCTCTGTTCT
 GCAAACCtgt ggggaaaaga aagatcagat tgttactgtg tctacgtaga aaatgaagac
 ataagaaact ccattttgaa ctgtactaag aaaaattgtt tctgctttga gatgctatta
 acctgtaact ttagccccaa ccgtgtgctc acagaaacat gtcctgtatt gaatcaaagt
 ttaatggatt tagggctttg caggatgtgc cttgttaaca atatgtttgc aggcagtatg
 cttggtaaaa gtcatcgcca

  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_011109
dbSNP Blast Analysis
UniGene Cluster ID
405755

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 G/G
 HWP C
 G
ss14691157 HapMap-CEU European 120 IG 0.017 0.983 1.000 0.008 0.992
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 90 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.083 0.317 0.600 0.294 0.242 0.758
ss23812946 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.348 0.652 0.317 0.174 0.826
AFD_CHN_PANEL Asian 48 IG 1.000 1.000
ss48404983 AGI_ASP population multiple 70 IG 0.029 0.114 0.857 0.150 0.086 0.914
ss69229883 HapMap-CEU European 120 GF 0.033 0.967 0.017 0.983
HapMap-HCB Asian 88 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.083 0.283 0.633 0.225 0.775
Concordant Genotype Total Sample C/C C/G G/G
ss14691157 521 8 24 233
ss23812946 71 8 63
ss48404983 38 1 4 30
RefSNP Genotype Summary Total Individual C/C C/G G/G
rs10401800 619 9 36 317
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
169 ss14691157 G/G CSHL-HAPMAP HapMap-CEU NA06994 CEPH1340.09 r27_ch19_CEU_perlegen:genotyping_1.0.0 5607840
5142 ss14691157 C/G CSHL-HAPMAP HapMap-YRI NA19194 YOR112.01 r27_ch19_YRI_perlegen:genotyping_1.0.0 5607840
5237 ss14691157 C/G CSHL-HAPMAP HapMap-YRI NA18501 YOR004.03 r27_ch19_YRI_perlegen:genotyping_1.0.0 5607840
5293 ss14691157 C/G CSHL-HAPMAP HapMap-YRI NA19159 YOR056.02 r27_ch19_YRI_perlegen:genotyping_1.0.0 5607840
Genotype data submitted for634 samples from619 individualsIndividual with multiple genotypes submission:15

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 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 .