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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs5933536          
refSNP ID: rs5933536
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:114/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_015075.1:c.123-6643A>C
NT_011630.14:g.845972T>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 ss8213600 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5933536 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
ss8213600SC_SNP|NT_011799.10_172475byFreqfwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac04/16/0310/25/06114Genomicunknown
ss20397921CSHL-HAPMAP|CSHL-HuFF-200402.chrX.NT_011630.14_845972fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac02/21/0403/04/04120Genomicunknown
ss21057814SSAHASNP|WGSA-200403-chrX.chrX.NT_011630.14_845972fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac03/19/0403/19/04121Genomicunknown
ss67427047ILLUMINA|HumanHap550v1.1_rs5933536fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac11/14/0611/14/06127Genomicunknown
ss67785214ILLUMINA|HumanHap650Yv1.0_rs5933536fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac11/14/0611/14/06127Genomicunknown
ss68245420ILLUMINA|HumanHap250Sv1.0_rs5933536fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac12/06/0612/07/06127Genomicunknown
ss70850428ILLUMINA|HumanHap550v3.0__rs5933536fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac04/20/0703/31/08130Genomicunknown
ss71435645ILLUMINA|HumanHap650Yv3.0_rs5933536fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac04/23/0704/23/07127Genomicunknown
ss74940340ILLUMINA|ILMN_Human_1M_rs5933536fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac08/28/0708/29/07129Genomicunknown
ss77591533HGSV|Cor12156_SNV_20070510.chrX_53174907fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac10/09/0710/13/07129Genomicunknown
ss78440011HGSV|Cor12878_SNV_20070510.chrX_53174907fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac10/17/0710/19/07129Genomicunknown
ss83381425HGSV|Cor18555_SNV_20070510.chrX_53174907fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac11/27/0712/04/07130Genomicunknown
ss84433401KRIBB_YJKIM|KHS709779fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac12/04/0712/07/07130Genomicunknown
ss94285745BCMHGSC_JDW|JWB-2679562fwd/BG/Tccaatcccagtgtcacagggatctaagcccagcccagcctggcttggcacaggaactgac02/26/0803/06/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs5933536|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 CTCCTTCCCT TTATTGGCAC TGCCCGGAAC CAGGCAGCCA GCAGGGGATG GGATCAGGAT
 GCAGTTGTCA TGGAAACGAA TGGGGGCTGT TGCCATGGAT ATCATAAGAT GAGGGCAAGA
 GGAAGCTAGG GATGGTGAGG ACTATCCCCA TGACAACTTA GGTGGCAGTG GGGGGAACGG
 GACGGACTGG AAGTAGAGAC AAGAAAACAA GACGAGGAAG GTCATTGCAC CTGGATGGGA
 CCAGGGGCTT TGGGTTCTGG AAGGAGCAGA CTGGGCCAGG AGACTGGACC CAGTGGCAGG
 GGAGAGAGGA GGCAGGGGGA CTGCAGCCAC CTCTCCCTCC AATATTTCTT CTGCAAGCTA
 GTTCTGCTGC CCAATCCCAG TGTCACAGGG ATCTAAGCCC
 K
 AGCCCAGCCT GGCTTGGCAC AGGAACTGAC AGGGAAGAAA GCAGCCTTCA GAGGAGCTGA
 GCTGCATACA CGGGCTTTGG GAGCGCAAGA CCTGAGCTTG AATCCCAGCT TTGCTGCTGT
 GCAGCCCTAA AAATAATAGT TGTCATTTAT TGAGTTGTCA TTTTGCTAGG CTGAGCAACA
 CTGCAAGGTT TGGGTTGTTC TCTCTGAGGA GGACAGCaca gatgatgaaa ctgaggtaca
 gagagatgaa gtaacctgcc caaagccttg aagctcagca ctggtggagc caagattcaa
 acaaaagtgt atctgaacac aaagcccgtg ctcttaccac caCCCCACCC TCTGTCCCAG
 GCACTATAAG CAGTCCCTTC AAGGTACAGT CCTCGCATTC

  GeneView back to top
GeneView via analysis of contig annotation: IQSEC2 IQ motif and Sec7 domain 2
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_011630->NM_015075
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011630->NM_015075->NP_055890845972reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs5933536 maps exactly once on NCBI human chromosome X
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
XNW_001842369.147176450357193plusGalt_assembly_8HuRefHuRefview400
XNT_011630.1484597253308611plusTref_assemblyreferencereferenceview400
XNW_927709.128234857121110plusGalt_assembly_1CeleraCeleraview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011799
dbSNP Blast Analysis
GenBank HTGS Finished:
AL139396.18

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceG/G
G/T
T/T
HWPG
T
ss8213600HapMap-CEUEuropean 120IG 0.983 0.017 0.752 0.992 0.008
HapMap-HCBAsian 90IG 0.689 0.156 0.156 0.200 0.767 0.233
HapMap-JPTAsian 88IG 0.682 0.068 0.250 0.050 0.716 0.284
HapMap-YRISub-Saharan African 120IG 0.950 0.033 0.017 1.000 0.967 0.033

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.214+/-0.24727021000

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

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Revised: May 25, 2006 1:38 PM .