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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs28912985          
refSNP ID: rs28912985
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:125/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_000547.3:c.2386+2190A>G
NM_175719.1:c.2215+2190A>G
NM_175721.1:c.2386+2190A>G
NM_175722.1:c.1867+2190A>G
NT_022221.12:g.226663A>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 ss37044031 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28912985 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
ss37044031EGP_SNPS|TPO-087475byFreqfwd/TA/Gttaaggaattgatggcaggtgcttcagggttagcatgttgcgtgttctacgttaacaagc04/20/0511/02/06125Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs28912985|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=125
 CGGTGATAGA AACACAACTA CTCTGTCGGG TGATGACATC TGTGTAAACT CGTGGTTGCT
 GTTAACACTA TTGCATGACT CCTGACCATA GGCTCTGCCA CTGACCCTTC AGTGACAAAA
 GGGTCACGAA TCGCAAGGTT TTCCTGTTCC CTTGGCTTAG AGACTGCACA AACTTGAAAC
 GGCCACTTCA CCCACGATTC CTGGTTTTCC GTGTTGGCAT TACAGTTAAG GAATTGATGG
 CAGGTGCTTC AGGGT
 R
 TAGCATGTTG CGTGTTCTAC GTTAACAAGC CTTCCTATGG TGCACTTCAC TGTACACCTG
 CGTCTCTCCT TGCCCAAATA CCCAGACGTT TCACGTGTCC ATTTTAGCTT CATTTTAAGT
 ATGAATGACC CCAAAGTGCT ACTCACAGGC ATCTTCAAGG TGCAAATAAA AGATGGGTGA
 GACCTTAGAG TGGATCAGGA AGGGAGACTG CTGGAGTCCT ACAACCTGCC TGTGTGGAGC
 TGCCCCCTGT GCGCG

  GeneView back to top
GeneView via analysis of contig annotation: TPO thyroid peroxidase
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_022221->NM_000547
svfunction
referenceNT_022221->NM_175719
svfunction
referenceNT_022221->NM_175721
svfunction
referenceNT_022221->NM_175722
svfunction
HuRefNW_001838759->NM_000547
svfunction
HuRefNW_001838759->NM_175719
svfunction
HuRefNW_001838759->NM_175721
svfunction
HuRefNW_001838759->NM_175722
svfunction
CeleraNW_927719->NM_000547
svfunction
CeleraNW_927719->NM_175719
svfunction
CeleraNW_927719->NM_175721
svfunction
CeleraNW_927719->NM_175722
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_022221->NM_000547->NP_000538226663forwardintron
referenceNT_022221->NM_175719->NP_783650226663forwardintron
referenceNT_022221->NM_175721->NP_783652226663forwardintron
referenceNT_022221->NM_175722->NP_783653226663forwardintron
HuRefNW_001838759->NM_000547->NP_000538214756forwardintron
HuRefNW_001838759->NM_175719->NP_783650214756forwardintron
HuRefNW_001838759->NM_175721->NP_783652214756forwardintron
HuRefNW_001838759->NM_175722->NP_783653214756forwardintron
CeleraNW_927719->NM_000547->NP_0005381482706forwardintron
CeleraNW_927719->NM_175719->NP_7836501482706forwardintron
CeleraNW_927719->NM_175721->NP_7836521482706forwardintron
CeleraNW_927719->NM_175722->NP_7836531482706forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs28912985 maps exactly once on NCBI human chromosome 2
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
2NT_022221.122266631481734plusAref_assemblyreferencereferenceview255
2NW_001838759.12147561493142plusAalt_assembly_8HuRefHuRefview255
2NW_927719.114827061550771plusAalt_assembly_1CeleraCeleraview255

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
DQ011222
dbSNP Blast Analysis
GenBank HTGS Finished:
AC105450.1 NC_000002.10

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss37044031EGP_YORUB-PANELSub-Saharan African 24IG 0.583 0.417 0.371 0.792 0.208
EGP_HISP-PANELHispanic 42IG 1.000 1.000
EGP_CEPH-PANELEuropean 42IG 1.000 1.000
EGP_AD-PANELAfrican American 30IG 0.667 0.200 0.133 0.100 0.767 0.233
EGP_ASIAN-PANELAsian 46IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.122+/-0.215959500

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byFreqUNKNOWNUNKNOWNYES

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Revised: May 25, 2006 1:38 PM .