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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs228275          
refSNP ID: rs228275
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_002795.2:c.188+1238C>T
NT_010755.15:g.635121C>T
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 ss1939792 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs228275 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
ss295606KWOK|OVLP-000621-295105fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa06/30/0010/10/0379Genomic97 %
ss780884SC_JCM|AC024189.3_158446fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa07/27/0010/10/0387Genomicunknown
ss1019076KWOK|OVLP-000804-270403fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa09/02/0010/10/0386Genomic97 %
ss1939792KWOK|OVLP-000925-6180byFreqfwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa10/06/0004/07/0487Genomic97 %
ss20033979CSHL-HAPMAP|CSHL-HuFF-200402.chr17.NT_010755.14_635121fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa02/21/0403/04/04120Genomicunknown
ss21429701SSAHASNP|WGSA-200403-chr17.chr17.NT_010755.14_635121fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa03/19/0403/20/04121Genomicunknown
ss44022085ABI|hCV550289fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa07/18/0507/18/05126Genomicunknown
ss66775574ILLUMINA|HumanHap300v1.1_rs228275fwd/TC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa11/09/0611/09/06127Genomicunknown
ss67241744ILLUMINA|HumanHap550v1.1_rs228275fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa11/14/0611/14/06127Genomicunknown
ss67638486ILLUMINA|HumanHap650Yv1.0_rs228275fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa11/14/0611/14/06127Genomicunknown
ss70720092ILLUMINA|HumanHap550v3.0__rs228275fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa04/20/0703/30/08130Genomicunknown
ss71288416ILLUMINA|HumanHap650Yv3.0_rs228275fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa04/23/0704/23/07127Genomicunknown
ss75761747ILLUMINA|ILMN_Human_1M_rs228275fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa08/28/0708/29/07129Genomicunknown
ss79126229ILLUMINA|HumanHap300v2.0_rs228275fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa04/18/0711/18/07130Genomicunknown
ss83394174KRIBB_YJKIM|KHS451156fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa12/04/0712/04/07130Genomicunknown
ss90583032BCMHGSC_JDW|JWB-1019376fwd/BC/Tataacacttactgagatctcacccagcctgccttttttcctgtctggtagagtcagagaa02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs228275|allelePos=513|totalLen=817|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GTCACAGGGG GCAGGTCCTG CAGGGTACTG GTGCCTGAGG AGCAGCAGGT CCTGGATTTG
 TTTCCTAGAA GGTGGAGAGA CTAGCTCACA AGCGTGGGTG GATGCCTGTC AGAAAATGTT
 CTCATTTCgg ctgggcgcgg tggctcacac ctgtaatccc aacactttgg gaggctgagg
 tgggcggata tcttgagatc aggagttcca gaccagcctg gccaacatgg tgaaacgctg
 tctctactaa aaatacaaaa attagccagg ctgggtggtg ggcacctgta atcccagcta
 ctcgggaggc tgaggctgga gaattgcttg aacctgacag acggacgttg cagtgagctg
 aaattgtgcc actgcactct agcctgggca acagagcgag actctgtctc aaacaaaata
 aaaaaagaaa gaataaaaGA AAATGTTCTC ATTTCTCTTA AAACTCCCTG AGTCTCAAGA
 ACATAACACT TACTGAGATC TCACCCAGCC TG
 Y
 CCTTTTTTCC TGTCTGGTAG AGTCAGAGAA TGACATCCTG GGGTTCCTGT CAGTGAAGTC
 TCCCGTGAGC CTTCCCTTCT GCAGTCACTG CTGTTCTCAC ACCATTTCCT TTTCTTCAGA
 GGGCTTTTCT CACTGCGTTT GCTTCCTTCt gggcaatgac tgctcatttc actaggcctc
 agtttcctta cctggaagat gaagCTCAAG TCATTTCTAA GTCTCTTTGC TCTGGTGTCC
 TGAGACTCAT TGCTTTTCCT CCAGCAGGTG TGGCATTGGT CTGCTCTATG CAGGGGCCTA
 TCCT

  GeneView back to top
GeneView via analysis of contig annotation: PSMB3 proteasome (prosome, macropain) subunit, beta type, 3
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_010755->NM_002795
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010755->NM_002795->NP_002786635121forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs228275 maps exactly once on NCBI human chromosome 17
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
17NW_001838435.2284594332706916minusGalt_assembly_8HuRefHuRefview512
17NW_926828.144297633571785plusTalt_assembly_1CeleraCeleraview512
17NT_010755.1563512134164351plusCref_assemblyreferencereferenceview512

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010755 AC006449 AC024189.3
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1939792CEPH 184AF 0.570 0.430
HapMap-CEUEuropean 120IG 0.383 0.533 0.083 0.200 0.650 0.350
HapMap-HCBAsian 90IG 0.133 0.489 0.378 1.000 0.378 0.622
HapMap-JPTAsian 88IG 0.091 0.409 0.500 1.000 0.295 0.705
HapMap-YRISub-Saharan African 120IG 0.767 0.217 0.017 1.000 0.875 0.125

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.487+/-0.08027021000

  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: ILLUMINA
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .