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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2230050          
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:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
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 ss105435175 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2230050 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
ss3177141WICVAR|WI-17840byFreqfwd/BC/Tagagggtgggagaaactcccctgatgaatgggactccatcttggctgtgaagaaatactt06/28/0104/07/0498cDNAunknown
ss48397523EGP_SNPS|IFNA1-002466byFreqfwd/BC/Tagagggtgggagaaactcccctgatgaatgggactccatcttggctgtgaagaaatactt08/30/0511/03/06130Genomicunknown
ss105435175SNP500CANCER|IFNA1-08fwd/BC/Tagagggtgggagaaactcccctgatgaatgggactccatcttggctgtgaagaaatactt09/05/0809/05/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2230050|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CCTTGATGCT CCTGGCACAA ATGAGCAGAA TCTCTCCTTC CTCCTGTCTG ATGGACAGAC
 ATGACTTTGG ATTTCCCCAG GAGGAGTTTG ATGGCAACCA GTTCCAGAAG GCTCCAGCCA
 TCTCTGTCCT CCATGAGCTG ATYCAGCAGA TCTTCAACYW CTTTACCACA RAAGATTCAT
 CTGCTGCTTG GGATGAGGAC CTCCTAGACA AATTCTGCAC CGAAMTCTAC CAGCAGCTGA
 ATGACTTGGA AGCCTGTGTG ATGCAGGAGG AGAGGGTGGG AGAAACTCCC CTGATGAATG
 Y
 GGACTCCATC TTGGCTGTGA AGAAATACTT CCGAAGAATC ACTCTCTATC TGACAGAGAA
 GAAATACAGC CCTTGTGSCT GGGAGGTTGT CAGAGCAGAA ATCATGAGAT CCCTCTCTTT
 ATCAACAAAC TTGCAAGAAA GATTAAGGAG GAAGGAATAA YAYCTGGTCC AACATGAAAN
 CAATTCTTAT TGACTCATAY ACCAGGTCAC GCTTTCATGA ATTCTGTCAT TTCAAAGACT
 CTCACYCCTG CTATAACTAT GACCATGCTG ATAAACTGAT TTATCTATTT AAATATTTAT

  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_006900
dbSNP Blast Analysis
UniGene Cluster ID
37026 533471

  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
ss105435175 P1 202 GF 0.931 0.069 0.965 0.035
CAUC1 62 GF 1.000 1.000
AFR1 46 GF 0.783 0.217 0.891 0.109
HISP1 46 GF 0.957 0.043 0.978 0.022
PAC1 48 GF 0.958 0.042 0.979 0.021
P2 418 GF 0.871 0.124 0.005 0.933 0.067
CAUC2 118 GF 0.966 0.034 0.983 0.017
AFR2 120 GF 0.667 0.317 0.017 0.825 0.175
ASI2 180 GF 0.944 0.056 0.972 0.028
ss3177141 MITOGPOP6 multiple 64 IG 0.969 0.031 0.001 0.969 0.031
ss48397523 EGP_YORUB-PANEL Sub-Saharan African 22 AF 0.636 0.364 0.479 0.818 0.182
EGP_HISP-PANEL Hispanic 40 AF 1.000 1.000
EGP_CEPH-PANEL European 28 AF 1.000 1.000
EGP_AD-PANEL African American 20 AF 0.800 0.200 0.752 0.900 0.100
EGP_ASIAN-PANEL Asian 48 AF 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.101+/-0.201 126 126 1 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 .