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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs540636          
refSNP ID: rs540636
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:83/129
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
NM_001040445.1:c.*3189T>C
NT_005120.15:g.5291095T>C
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 ss44301525 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs540636 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
ss711351SC_JCM|AC011973.3_152887fwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt07/27/0010/10/0383Genomicunknown
ss1100115KWOK|OVLP-000804-189559fwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt09/02/0010/10/0386Genomic99 %
ss1707493KWOK|OVLP-000925-554942fwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt10/05/0010/10/0387Genomic99 %
ss6421248WI_SSAHASNP|NT_005120.11_5288548fwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt02/12/0310/10/03111Genomicunknown
ss19441265CSHL-HAPMAP|CSHL-HuDD-200402.chr2.NT_005120.14_5288811fwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt02/20/0403/04/04120Genomicunknown
ss21573525SSAHASNP|WGSA-200403-chr2.chr2.NT_005120.14_5288811fwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt03/20/0403/20/04121Genomicunknown
ss44301525ABI|hCV1295443byFreqfwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt07/18/0508/14/07126Genomicunknown
ss65743256ILLUMINA|Human1-rs540636fwd/TC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt10/10/0610/10/06127Genomicunknown
ss74903520ILLUMINA|ILMN_Human_1M_rs540636fwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt08/28/0708/29/07129Genomicunknown
ss91600908BCMHGSC_JDW|JWB-1404733fwd/BC/Tcttgttccagaaaagtgtttaaggcaacaagcttgttttttggtgttttcttttgacatt02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs540636|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GGAGCCTGAA GGTTGCCCCT GGTTGCATCC CAGAAGCATC TGACTGTCAC CACTGCCAGT
 GGCTGTGGAA CAGTCCTGGG CCCTGGGCCT TGGCTGCTGT CAACAGATGG GCTGGGCTGG
 GCTGTGGTGG GGTGGGGGAC AACGTTGGTA ACTCTGAGAA TTCAGCTTTG GAGTCCCGGG
 TGAGGGGTTT TAGATAAACC CATCAATATC ACCCACATTC TGTGACTCTT TGCATCACTC
 GTGTTATTTA TTTATTTATT TATATTCTGC CTTGTTCCAG AAAAGTGTTT AAGGCAACAA
 Y
 GCTTGTTTTT TGGTGTTTTC TTTTGACATT TGAAAATTTA GTACATTGTT AAAATGTACT
 TGTTAAACAG GTAATTTTAA AGAGAAGGAA CAATTGTTTT TAGTAAGTTT TCTTTTTCCT
 TTTTCAATGA ATTGATTCTT CAAATTAAAA GTTCTTGAGA GAAGGAGAGG AAGATACAGC
 AGACATAGGA CTGAGCCAAG GAAGAGTCTG CCTGAGAGAG ACGCTTGGCC TGTGCTTTGC
 TGCCATCCGT GCGGCCTTGG CCACATCCCT ATTAACAGAG GCAGCTCCAC TTCAGACAGG

  GeneView back to top
GeneView via analysis of contig annotation: ASB1 ankyrin repeat and SOCS box-containing 1
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_005120->NM_001040445
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_005120->NM_001040445->5291095forward42833' UTR

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs540636 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
2NW_001838870.13275332231149395plusTalt_assembly_8HuRefHuRefview300
2NW_921618.143985357233070827plusCalt_assembly_1CeleraCeleraview300
2NT_005120.155291095239023080plusTref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005120 AC016999 AC016999.5
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank mRNA:
NM_001040445.1 AB032972.1
UniGene Cluster ID
516788

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss44301525HapMap-CEUEuropean 116IG 0.397 0.379 0.224 0.586 0.414
HapMap-HCBAsian 90IG 0.111 0.444 0.444 0.333 0.667
HapMap-JPTAsian 88IG 0.091 0.523 0.386 0.352 0.648
HapMap-YRISub-Saharan African 118IG 0.136 0.864 0.068 0.932

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.444+/-0.15827021000

  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, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .