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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs227368          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C/G/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_005908.3:c.757G>A
NM_005908.3:c.757G>C
NM_005908.3:c.757G>T
NP_005899.3:p.Val253Ile
NP_005899.3:p.Val253Leu
NT_016354.18:g.28159590C>A
NT_016354.18:g.28159590C>G
NT_016354.18:g.28159590C>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 ss44484881 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs227368 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
ss294522KWOK|OVLP-000621-289978rev/BC/Ttctgttgtgtttgcaacttagggatggctagatcacttgaccaccaactggctttgagct06/30/0010/10/0379Genomic97 %
ss580139SC_JCM|AC024629.1_111183fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga07/12/0010/10/0380Genomicunknown
ss1042329KWOK|OVLP-000804-566978fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga09/02/0010/10/0386Genomic97 %
ss1948550KWOK|OVLP-000925-207548fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga10/06/0010/10/0387Genomic97 %
ss2317436TSC-CSHL|TSC0725509byFreqfwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga06/14/0110/25/06110Genomicunknown
ss22210764SSAHASNP|WGSA-200403-chr4.chr4.NT_016354.16_28106574rev/BC/Ttctgttgtgtttgcaacttagggatggctagatcacttgaccaccaactggctttgagct03/20/0403/21/04121Genomicunknown
ss38338863PERLEGEN|PS00646283fwd/BC/Tagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga05/09/0505/09/05125Genomicunknown
ss44484881ABI|hCV8935318byFreqrev/BC/Ttctgttgtgtttgcaacttagggatggctagatcacttgaccaccaactggctttgagct07/19/0511/03/06126Genomicunknown
ss66806535ILLUMINA|HumanHap300v1.1_rs227368fwd/BA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga11/09/0611/09/06127Genomicunknown
ss67240234ILLUMINA|HumanHap550v1.1_rs227368fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga11/14/0611/14/06127Genomicunknown
ss67636852ILLUMINA|HumanHap650Yv1.0_rs227368fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga11/14/0611/14/06127Genomicunknown
ss68906814PERLEGEN|PGP00646283byFreqrev/BC/Ttctgttgtgtttgcaacttagggatggctagatcacttgaccaccaactggctttgagct01/30/0708/14/07127Genomicunknown
ss70718574ILLUMINA|HumanHap550v3.0__rs227368fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga04/20/0703/30/08130Genomicunknown
ss71286773ILLUMINA|HumanHap650Yv3.0_rs227368fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga04/23/0704/23/07127Genomicunknown
ss74809307AFFY|SNP_M-182117fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga08/09/0708/09/07128Genomicunknown
ss75834746ILLUMINA|ILMN_Human_1M_rs227368fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga08/28/0708/29/07129Genomicunknown
ss79125075ILLUMINA|HumanHap300v2.0_rs227368fwd/TA/Gagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga04/18/0711/18/07130Genomicunknown
ss83393743KRIBB_YJKIM|KHS451053fwd/A/C/G/Tagctcaaagccagttggtggtcaagtgatctagccatccctaagttgcaaacacaacaga12/04/0712/04/07130Genomicunknown
ss86032033HGSV|Cor18956_SNV_20070510.chr4_103969048rev/BC/Ttctgttgtgtttgcaacttagggatggctagatcacttgaccaccaactggctttgagct11/30/0712/11/07130Genomicunknown
ss92711149BCMHGSC_JDW|JWB-1828064rev/BC/Ttctgttgtgtttgcaacttagggatggctagatcacttgaccaccaactggctttgagct02/26/0803/03/08129Genomicunknown
ss98988701HUMANGENOME_JCVI|1103654502060rev/BC/Ttctgttgtgtttgcaacttagggatggctagatcacttgaccaccaactggctttgagct04/02/0804/02/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs227368|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/C/G/T'|mol=Genomic|build=130
 AAAATATATC ATTTTTGTTA TTCTTCTTCA GAATGAAGGA TTAAACTGAA GATTAAAAGA
 AAATTTCCAC GAAGTTTTGA TTATGACAGC ATTGTGGAGC ACGTACTGGG TTTGAAGCTG
 CTTTAGTATT ACCTTCAATG AATCCTGAGA AATGCAGTGA TAATGCTTAG CATATTATAT
 ATATATATAT ATATTTCTTT TTCTTTTTAT ATTTTAGATA AGAGTGCCCA GGAGTGGAAT
 CTGGAAATAG AGTCTACATT TGATGTTGTC AGCTCAAAGC CAGTTGGTGG TCAAGTGATC
 N
 TAGCCATCCC TAAGTTGCAA ACACAACAGA CATACAGCAT TGAACTTCAA CCTGGGAAAA
 GGATTGTTGA GCTATTTGTG AACATTAGCA AGGTAAATGA TGGTACTTCC TGAGAAGCAC
 TGGATGAAAA GCAATACCTG TGCTAAAGAA ATGATTAGAA AGGAGGGACT AAGTATGAAA
 GAAAATTCTA CTTTCTCTGC TTATATTTGT CATTTTCTTC TCTATTTTAG TCTCTCATAT
 ATTTTCTGTG AGTATGAGCT AAAGAATGAT TTTCCCAAAC TTTAAGATTA AGAAAATAGA

  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_016354 ABBA01063702 AF224669 AF224669.1
dbSNP Blast Analysis
UniGene Cluster ID
480415

  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
ss2317436 EURAME 32 GF 0.062 0.750 0.188 0.050 0.438 0.562
AFRAME 32 GF 0.062 0.312 0.625 0.752 0.219 0.781
ss44484881 HapMap-CEU European 120 IG 0.183 0.533 0.283 0.584 0.450 0.550
HapMap-HCB Asian 90 IG 0.244 0.533 0.222 0.655 0.511 0.489
HapMap-JPT Asian 88 IG 0.318 0.455 0.227 0.584 0.545 0.455
HapMap-YRI Sub-Saharan African 120 IG 0.150 0.850 0.584 0.075 0.925
ss68906814 HapMap-CEU European 120 GF 0.183 0.533 0.283 0.450 0.550
HapMap-HCB Asian 90 GF 0.244 0.533 0.222 0.511 0.489
HapMap-JPT Asian 90 GF 0.333 0.444 0.222 0.556 0.444
HapMap-YRI Sub-Saharan African 120 GF 0.150 0.850 0.075 0.925

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.540+/-0.158 1208 1002 270 0

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

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Revised: May 25, 2006 1:38 PM .