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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs3856334          
refSNP ID: rs3856334
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:108/129
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
NM_002348.2:c.455-4444C>T
NT_004487.18:g.11269337C>T
Links

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 ss20519090 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3856334 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
ss2296761TSC-CSHL|TSC0396515fwd/BC/Tcaaattactgaatctaatggtatatgcatttttttttttttgagacatcatcccactaca06/14/0110/10/03108Genomicunknown
ss5356645TSC-CSHL|TSC1530132fwd/BC/Tcaaattactgaatctaatggtatatgcatttttttttttttgagacatcatcccactaca09/20/0210/10/03108Genomicunknown
ss5428906TSC-CSHL|TSC1374667fwd/BC/Tcaaattactgaatctaatggtatatgcatttttttttttttgagacatcatcccactaca09/20/0210/10/03110Genomicunknown
ss6221926SC_JCM|NT_004982.12_2687579fwd/BC/Tcaaattactgaatctaatggtatatgcatttttttttttttgagacatcatcccactaca01/10/0310/10/03111Genomicunknown
ss20519090SSAHASNP|WGSA-200403-chr1.chr1.NT_079484.1_7228814fwd/BC/Tcaaattactgaatctaatggtatatgcatttttttttttttgagacatcatcccactaca03/18/0403/18/04121Genomicunknown
ss41064825ABI|hCV7477492fwd/BC/Tcaaattactgaatctaatggtatatgcatttttttttttttgagacatcatcccactaca07/16/0507/17/05126Genomicunknown
ss87839363BCMHGSC_JDW|JWB-0133834fwd/BC/Tcaaattactgaatctaatggtatatgcatttttttttttttgagacatcatcccactaca02/26/0802/26/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3856334|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 ctgttgaatt ccagcattct cccttggaaa atgtatttga aatatgactg tttgtatact
 acttttgttc ttctaagtag aggaggtagg cattaaatgc ttctagtcag ccatttcgaa
 gccccttctC TTGATCTTTT ATTTTTAAAA ACAGACATTC TTTTTCTCCA GGAATTTCTC
 TCTCTAGGAT AAATATGACT ACTATATTGA TCGTTTTTCA CCTAATTCCA TATACACAGA
 TGTCAAAATT AGAAGACACA CCCGTAAATT CCTTACATGT TATATAATCG CCATAATTCA
 TGTAACGGGT CTCCTACTTG TAGAAATATT GTTTctgctt atagaaatat tgtttccaat
 atttcctctt ataaacaatg ctgcaatgaa tattcttgtg cacctatctt ttcacgctta
 tgtgactagg ttatattctg atggataaat ctagaaTATA TATATGGGGT CAAATTACTG
 AATCTAATGG TATATGCAtt
 Y
 tttttttttt tgagacatca tcccactaca tcacctaggc ttgcctccaa ttcctgggct
 caagtgatcc tcctgcctct atcttccaag tagctgggac tacaggtact tgccaccatg
 cccagcTTTT AAATCCTGAA Tttattatta ttattattat tattattatt actactacta
 ttaCCAGTAT TTCATAGAGA CATAGTCTCA TTTTGTTGTC CAGGCTagtc gcaaactcct
 ggactcaagc tgtccccttc cctcaacctc ccaagtagct gggactacag gcatgtgcca
 ccatgcctgg ctttaaaatc ctcaattttt atttattatt attttatttt gtagagactg
 gttctcacta tgttgcccag gctgattcca aactcctggc ctcaaacaat ccttccacct
 cagcctccaa agaagctggt attacaggca ccactgcacc tagctTAGTA TATACATTTT
 TAATGTTGCT AGATATTGCT

  GeneView back to top
GeneView via analysis of contig annotation: LY9 lymphocyte antigen 9
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_004487->NM_002348
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_004487->NM_002348->NP_00233911269337forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs3856334 maps exactly once on NCBI human chromosome 1
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
1NW_001838531.2631318^631319132135139^132135140minus-alt_assembly_8HuRefHuRefview500..500
1NW_925683.110884479133847653plusCalt_assembly_1CeleraCeleraview500
1NT_004487.1811269337159045606plusCref_assemblyreferencereferenceview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_079484
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL354714.22 CR759926.3

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
with2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .