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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2228093          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/130
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_000692.3:c.257C>T
NP_000683.3:p.Ala86Val
NT_008413.17:g.38386002C>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 ss76894958 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2228093 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
ss3172733WIAF-CSNP|WIAF-12954byFreqfwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat06/19/0104/07/0498cDNAunknown
ss6312102RIKENSNPRC|ssj0004484fwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat01/15/0310/10/03111Genomicunknown
ss15542436SC_SNP|NT_008413.16_38386002fwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat11/14/0311/22/03120Genomicunknown
ss24092964PERLEGEN|afd4596962byFreqfwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat08/10/0409/13/04123Genomicunknown
ss48430061APPLERA_GI|hCV16170569byFreqfwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat10/02/0511/03/06126Genomicunknown
ss65730971ILLUMINA|Human1-rs2228093fwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat10/10/0610/10/06127Genomicunknown
ss74875188ILLUMINA|ILMN_Human_1M_rs2228093fwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat08/28/0708/29/07129Genomicunknown
ss76894958SI_EXO|NT_008413.17_38386002fwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat09/20/0709/20/07129Genomicunknown
ss86344123CANCER-GENOME|14220fwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat01/25/0801/25/08129Genomicunknown
ss115729684ILLUMINA-UK|NA18507_000060097_NCBI36.1_chr9_38386002fwd/BC/Ttggatcgggccgtgaaagcagcccgggaagcttccgcctggggtccccatggcgccggat01/15/0901/16/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2228093|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GCTCTTACAG TCTGTGTTTT TAGAGGTGAC AGTCCTTTAT GCTGGAATCT TGAAATGTTT
 GAGCTGGTGG GCCCTTGGGT ACCGCCACCT GCCTTCTCCC ACCTGTTCAC CCTGGTTTCT
 TTTGTCCCTC TCCAGAGTGT CAGCATGCTG CGCTTCCTGG CACCCCGGCT GCTTAGCCTC
 CAGGGCAGGA CCGCCCGCTA CTCCTCGGCA GCAGCCCTCC CAAGCCCCAT TCTGAACCCA
 GACATCCCCT ACAACCAGCT GTTCATCAAC AATGAATGGC AAGATGCAGT CAGCAAGAAG
 ACCTTCCCGA CGGTCAACCC TACCACCGGG GAGGTCATTG GGCACGTGGC TGAAGGTGAC
 CGGGCTGATG TGGATCGGGC CGTGAAAGCA GCCCGGGAAG
 Y
 CTTCCGCCTG GGGTCCCCAT GGCGCCGGAT GGATGCCTCT GAGCGGGGCC GGCTGCTGAA
 CCGCCTGGCA GACCTAGTGG AGCGGGATCG AGTCTACTTG GCCTCACTCG AGACCTTGGA
 CAATGGGAAG CCTTTCCAAG AGTCTTACGC CTTGGACTTG GATGAGGTCA TCAAGGTGTA
 TCGGTACTTT GCTGGCTGGG CTGACAAGTG GCATGGCAAG ACCATCCCCA TGGATGGCCA
 GCATTTCTGC TTCACCCGGC ATGAGCCCGT TGGTGTCTGT GGCCAGATCA TCCCGTGGAA
 CTTCCCCTTG GTCATGCAGG GTTGGAAACT TGCCCCGGCA CTCGCCACAG GCAACACTGT
 GGTTATGAAG GTGGCAGAGC AGACCCCCCT CTCTGCCCTG

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_008413.17
dbSNP Blast Analysis
UniGene Cluster ID
436219

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 C/C
 C/T
 G/G
 T/T
 HWP A
 C
 G
 T
ss24092964 AFD_EUR_PANEL European 48 IG 0.750 0.208 0.042 0.439 0.854 0.146
AFD_AFR_PANEL African American 42 IG 0.857 0.143 0.752 0.929 0.071
AFD_CHN_PANEL Asian 44 IG 0.273 0.409 0.318 0.403 0.477 0.523
ss3172733 WIAF-CSNP-MITOGPOP5 multiple 44 IG 0.864 0.136 0.001 0.864 0.136
ss48430061 HapMap-CEU European 116 IG 0.638 0.310 0.052 1.000 0.793 0.207
HapMap-HCB Asian 90 IG 0.244 0.622 0.133 0.556 0.444
HapMap-JPT Asian 88 IG 0.455 0.477 0.068 0.693 0.307
HapMap-YRI Sub-Saharan African 118 IG 0.814 0.169 0.017 0.898 0.102
AGI_ASP population multiple 78 IG 0.077 0.205 0.718 0.100 0.179 0.821
Concordant Genotype Total Sample A/A A/G C/C C/T G/G T/T
ss24092964 68 42 15 7
ss3172733 19 17 2
ss48430061 36 2 8 26
ss76894958 1204 737 372 64
RefSNP Genotype Summary Total Individual A/A A/G C/C C/T G/G T/T
rs2228093 1315 2 8 783 385 26 73
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
215 ss24092964 C/T PERLEGEN AFD_EUR_PANEL NA10857 71_IND_CHR_9
215 ss76894958 N/N CSHL-HAPMAP HapMap-CEU NA10857 CEPH1346.01 r27_ch9_CEU_illumina:human_1m_beadchip
348 ss24092964 C/T PERLEGEN AFD_EUR_PANEL NA10860 71_IND_CHR_9
348 ss76894958 N/N CSHL-HAPMAP HapMap-CEU NA10860 CEPH1362.01 r27_ch9_CEU_illumina:human_1m_beadchip
399 ss24092964 T/T PERLEGEN AFD_EUR_PANEL NA10830 71_IND_CHR_9
399 ss76894958 T/T CSHL-HAPMAP HapMap-CEU NA10830 CEPH1408.01 r27_ch9_CEU_illumina:human_1m_beadchip
1695 ss3172733 C/C WIAF-CSNP WIAF-CSNP-MITOGPOP5 CL77 06.18.01-a
1695 ss48430061 G/G APPLERA_GI AGI_ASP population NA14661 3 730489
1696 ss3172733 T/T WIAF-CSNP WIAF-CSNP-MITOGPOP5 CL78 06.18.01-a
1696 ss48430061 A/A APPLERA_GI AGI_ASP population NA14663 3 730489
1697 ss3172733 C/C WIAF-CSNP WIAF-CSNP-MITOGPOP5 CL79 06.18.01-a
1697 ss48430061 G/G APPLERA_GI AGI_ASP population NA14665 3 730489
Genotype data submitted for1339 samples from1315 individualsIndividual with multiple genotypes submission:24

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN YES YES

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Revised: May 25, 2006 1:38 PM .