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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1229585          
refSNP ID: rs1229585
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
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 ss1820825 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1229585 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
ss1820825KWOK|OVLP-000925-126515byFreqfwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca10/05/0004/07/0487Genomic97 %
ss2460164SC_JCM|AC006961.16_18468fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca11/03/0010/10/0392Genomicunknown
ss14409658WI_SSAHASNP|chr18.NT_025028.13_1696804fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca11/05/0311/22/03119Genomicunknown
ss24509446PERLEGEN|afd3158312byFreqfwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca08/10/0409/13/04123Genomicunknown
ss44057247ABI|hCV8921967fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca07/18/0507/18/05126Genomicunknown
ss66734335ILLUMINA|HumanHap300v1.1_rs1229585fwd/TC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca11/09/0611/09/06127Genomicunknown
ss66996303ILLUMINA|HumanHap550v1.1_rs1229585fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca11/14/0611/14/06127Genomicunknown
ss67173310ILLUMINA|HumanHap650Yv1.0_rs1229585fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca11/14/0611/14/06127Genomicunknown
ss69215594PERLEGEN|PGP03158312byFreqfwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca01/30/0708/14/07127Genomicunknown
ss70407585ILLUMINA|HumanHap300v2.0_rs1229585fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca04/18/0711/18/07127Genomicunknown
ss70562804ILLUMINA|HumanHap550v3.0__rs1229585fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca04/20/0703/30/08130Genomicunknown
ss71101741ILLUMINA|HumanHap650Yv3.0_rs1229585fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca04/23/0704/23/07127Genomicunknown
ss75693052ILLUMINA|ILMN_Human_1M_rs1229585fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca08/28/0708/29/07129Genomicunknown
ss83703665KRIBB_YJKIM|KHS523412fwd/BC/Tttggttttatcagctcacccaaactgaagagaaacactggctcctcgtgatgctgttgca12/04/0712/05/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1229585|allelePos=734|totalLen=934|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GGACAGACAG GCCCCAGGGA AGAAGGTGGT CTCTTCAGAT CCCACAGTAT GAGCCAGCTT
 CAACCATCTC CCTGACTTGG GTCACAGCTC TCTAGCTTCC gattgtgcct ggcctgctta
 aaaagcatca gggtgagtgt ggatggagcc aagtgagcat gagcagactg gaggatgatg
 gggtcggagg tcagacggag gaaccacagc ttgccaggcc tCAGAGTTAG TCGGGACACA
 CAcaggtagg gcatccctaa tccaaaaatc tgaaatccac aatgttcaaa aacctgaaac
 tttttgagca ctgatgtgat gtcacatgtg gaaaattcca cacctgactt cacatgacag
 gttgcagtca aaactatttt tcatgcacaa aattattgaa aatattgtat aaaattacct
 ttaggctttg tgtataaaat atatatgaaa catacataaa ttttccattt agatttgggt
 ctcatcccca agacatttca tgatgtttat agaaatattc caacatatga aaaaatacaa
 aatccgaacc gtctgatctc aagcattttg atcagagata ctcaacctAC GCTCAATTGG
 TAGCTATAAA AATCCCAAAT TGACAGAGGA AATAGTGATT AAATAACCCT CTTAAGTTTA
 AACAAGTGAG ATTTGACTCA AGACCTCCTT GCCTCTAAAG CTCTTGGTTT TATCAGCTCA
 CCCAAACTGA AGA
 Y
 GAAACACTGG CTCCTCGTGA TGCTGTTGCA ACACAGATGT GTCACCAGGT CCCCAAGATG
 ATATGTTAAG ATGGCTCCAT TTGTTGATGC CCAGTGGTAG TCAAGAGCAT TGCACCTTCC
 AGAAAAACAT GGAAGAACAG TTTTTTTGTT TGTTTGTTTT CCAGAATTTT AAGTAGAGCC
 AGGCCTCACG ATGGCACACA

  GeneView back to top
GeneView via analysis of contig annotation: LOC100133515 hypothetical protein LOC100133515
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
CeleraNW_927106->XM_001714560
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
CeleraNW_927106->XM_001714560->XP_0017146129216725reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1229585 maps exactly once on NCBI human chromosome 18
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
18NW_001838469.1169946150616112plusCalt_assembly_8HuRefHuRefview733
18NW_927106.1921672550623142plusTalt_assembly_1CeleraCeleraview733
18NT_025028.13169680452056938plusTref_assemblyreferencereferenceview733

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_025028 AP001909 AP001909.2 AP002786
dbSNP Blast Analysis
GenBank HTGS Draft:
AP001909.2 AP002786.1

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1820825HapMap-CEUEuropean 120IG 0.283 0.433 0.283 0.317 0.500 0.500
HapMap-HCBAsian 90IG 0.067 0.933 1.000 0.033 0.967
HapMap-JPTAsian 88IG 0.023 0.977 1.000 0.011 0.989
HapMap-YRISub-Saharan African 120IG 0.600 0.367 0.033 0.584 0.783 0.217
ss24509446AFD_EUR_PANELEuropean 48IG 0.167 0.500 0.333 1.000 0.417 0.583
AFD_AFR_PANELAfrican American 46IG 0.391 0.609 0.050 0.696 0.304
AFD_CHN_PANELAsian 48IG 0.042 0.958 1.000 0.021 0.979
ss69215594HapMap-CEUEuropean 120GF 0.283 0.433 0.283 0.500 0.500
HapMap-HCBAsian 90GF 0.067 0.933 0.033 0.967
HapMap-JPTAsian 90GF 0.022 0.978 0.011 0.989
HapMap-YRISub-Saharan African 120GF 0.600 0.367 0.033 0.783 0.217

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.470+/-0.1203322602700

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .