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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs12413168          
refSNP ID: rs12413168
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_152725.2:c.1269+229C>G
NT_008705.15:g.252134C>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 ss19166785 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12413168 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
ss19166785CSHL-HAPMAP|CSHL-HuDD-200402.chr10.NT_008705.15_252134byFreqfwd/TC/Gccacatagtagtagtatttttgaaataaaaaaaggaaaggtggcagggcacggtggctca02/20/0410/26/06120Genomicunknown
ss20656239SSAHASNP|WGSA-200403-chr10.chr10.NT_008705.15_252134fwd/TC/Gccacatagtagtagtatttttgaaataaaaaaaggaaaggtggcagggcacggtggctca03/18/0403/18/04121Genomicunknown
ss39729754ABI|hCV3159070fwd/C/Gccacatagtagtagtatttttgaaataaaaaaaggaaaggtggcagggcacggtggctca07/16/0507/16/05126Genomicunknown
ss83909319HGSV|Cor18555_SNV_20070510.chr10_18316815fwd/C/Gccacatagtagtagtatttttgaaataaaaaaaggaaaggtggcagggcacggtggctca11/27/0712/06/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12413168|allelePos=201|totalLen=701|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 AGTTCACTTC ATTGCTCTTC ACTTTTAACC ACTGGAGGTA TTTATGCAAA ATTTTACTGA
 GACTTCAAAG AGAGAGTATC GTGGCTGGTG TTTTCCTTAA AAAGAAATAT TATTTCCCCA
 AGGCCTCTCT GCACTTGTAG AAGAGAAGAG ATGCCCCAAC ATTAGGCTCG CCACATAGTA
 GTAGTATTTT TGAAATAAAA
 S
 AAAGGAAAGG Tggcagggca cggtggctca cacctgtaat cccagtacca tggaaggctg
 aggcgggaag atcgctggag cccaggagct caagaacagc ctggccgatg tggtggaacc
 ccatctctac taaaaataca aaaattagct gCACATGTTA CATGcaccgg tagtcccagc
 actttgggag gccaaggcag gtggattact tgagatcagg agttcgagac cagcctggac
 agcatggtga aaccccatct ctactaaaaa tataaaaatt agctgggcat agtgccatgc
 gtctgtaatc ctagctactc gggaggctga gacaggagaa tcgcttgaac tcgagaggcg
 aaggttgcag tgagcaaaga tcgtaccact gcactccagc atgggtgaca gagcgagact
 ctgtctcaga aaaagttgtc attcagttag ttcacccaag acctggttgt ttaaaagtcc
 agaacctccc cgtctccctc

  GeneView back to top
GeneView via analysis of contig annotation: SLC39A12 solute carrier family 39 (zinc transporter), member 12
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_008705->NM_152725
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_008705->NM_152725->NP_689938252134forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs12413168 maps exactly once on NCBI human chromosome 10
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
10NW_001837931.21283913317942844minusGalt_assembly_8HuRefHuRefview200
10NW_924584.11796331717963317plusCalt_assembly_1CeleraCeleraview200
10NT_008705.1525213418316815plusCref_assemblyreferencereferenceview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_008705
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL590111.14 AL157885.8

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/G
G/G
HWPC
G
ss19166785HapMap-CEUEuropean 116IG 0.345 0.397 0.259 0.150 0.543 0.457
HapMap-HCBAsian 86IG 0.465 0.465 0.070 0.527 0.698 0.302
HapMap-JPTAsian 90IG 0.578 0.333 0.089 0.439 0.744 0.256
HapMap-YRISub-Saharan African 118IG 0.271 0.644 0.085 0.020 0.593 0.407

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.464+/-0.12927021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .