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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs311927          
refSNP ID: rs311927
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:T
Clinical Association:unknown
HGVS Names
NM_024505.2:c.1945+2190G>A
NT_010194.16:g.40133907G>A
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 ss1896529 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs311927 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
ss400470KWOK|OVLP-000621-244163fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt06/30/0010/10/0379Genomic99 %
ss480201SC_JCM|AC027088.2_78968rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc07/12/0010/10/0380Genomicunknown
ss1174550KWOK|OVLP-000804-560934fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt09/02/0010/10/0386Genomic99 %
ss1896529KWOK|OVLP-000925-363456byFreqfwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt10/06/0010/25/0687Genomic99 %
ss3059906TSC-CSHL|TSC1147423rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc06/07/0110/10/0396Genomicunknown
ss3737392SC_JCM|AC026512.3_84214fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt09/25/0110/10/03100Genomicunknown
ss12332805WI_SSAHASNP|chr15.NT_010194.15_40132961rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc07/04/0310/10/03116Genomicunknown
ss16691103CSHL-HAPMAP|CSHL-HuAA-200402.chr15.NT_010194.16_40133907rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc02/17/0403/04/04120Genomicunknown
ss21283846SSAHASNP|WGSA-200403-chr15.chr15.NT_010194.16_40133907rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc03/19/0403/19/04121Genomicunknown
ss23415984PERLEGEN|afd4335131byFreqrev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc08/10/0409/13/04123Genomicunknown
ss67290919ILLUMINA|HumanHap550v1.1_rs311927fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt11/14/0611/14/06127Genomicunknown
ss67694483ILLUMINA|HumanHap650Yv1.0_rs311927fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt11/14/0611/14/06127Genomicunknown
ss68217973ILLUMINA|HumanHap250Sv1.0_rs311927fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt12/06/0612/07/06127Genomicunknown
ss70769503ILLUMINA|HumanHap550v3.0__rs311927fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt04/20/0703/30/08130Genomicunknown
ss71344611ILLUMINA|HumanHap650Yv3.0_rs311927fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt04/23/0704/23/07127Genomicunknown
ss75532499ILLUMINA|ILMN_Human_1M_rs311927fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt08/28/0708/29/07129Genomicunknown
ss77183582HGSV|Cor12156_SNV_20070510.chr15_67130642rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc10/09/0710/11/07129Genomicunknown
ss78597302HGSV|Cor18507_SNV_20070510.chr15_67130642rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc10/19/0710/20/07129Genomicunknown
ss81480247HGSV|Cor18555_SNV_20070510.chr15_67130642rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc11/27/0711/30/07130Genomicunknown
ss81917856HGSV|Cor18956_SNV_20070510.chr15_67130642rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc11/30/0712/01/07130Genomicunknown
ss83422761KRIBB_YJKIM|KHS458024fwd/BC/Tgactatcattgctgagagaagagaaacagagaagtaagccctacaacagccccgcttatt12/04/0712/05/07130Genomicunknown
ss90201328BCMHGSC_JDW|JWB-0873985rev/TA/Gaataagcggggctgttgtagggcttacttctctgtttctcttctctcagcaatgatagtc02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs311927|allelePos=686|totalLen=2457|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CATTCATTTT TGATAAAAGT ATAAAAGAAG GGACCAAACA GTTAATGACT TCATGTATGT
 TAAGGTATTT AATCTTTTTT TAAAAAAAAA ACAGGAATGG AAGGAAAAAG GGTGTCTAAT
 CTTTATCTTA GATCACTCTC TAAACTTTTT ATTCTCATTT CATCAGAAAA AAGGTTGAGC
 ACTCACCCCC CATAAATATA TATCTGTATC CATGTTTGTC TCTACTCACA GCTTGTGTAC
 ATCAAAAATG TATGTTGCAg gccaggtgca gtggtgcatg cctgtaatcc cagcactttg
 ggaggccaaa gctggtagat cacttgagct caggagttca agaccagcct gagtaacctg
 gagaaatctc atctacaaaa aatgagatta gctgggcatg gtggcgcaca cttgtactct
 cagttactta gcaggctgag atgggaggat cgcttgagcc cgggaggcag aggtggcagt
 gagcgccact gcactccaag ctgggtgatg gagacacact ctgtctcaaa aaaaaaaaga
 aaaaTTTACA TTGCCgtaaa atgaaccaca tttacccttc cacctgaaac aaccagaaaa
 atggacaaaa cacatgaaac aatggtttcc agacattgat cagcaggtgg cacgggacta
 tcattgctga gagaagagaa acaga
 Y
 gaagtaagcc ctacaacagc cccgcttatt gcctgatgca gtctcctgag gagaggagag
 gagacagaaa ctggcattca cagaggccag gacagccaga atgttaagca caagactgga
 aaagtgaact gcagaaagga agagagggaa ggtgggaagg agagaaggag agatgcaggg
 aggaggggag gcagggagga ggctactcac ttgctctgaa aatctgcata gtttctccta
 agtctctggc tgagcattaa tttgaatgtg tgaaagaaaa tgaccagaaa aactaggata
 aacgatacct cgagcttaaa cagctgggaa tagttggtgt tctcactaaa agcgaagagg
 ctttgccgta tatagcgcat taggtggagt cctcagaagt gtatcacctt agtactgggg
 ttaaattaat cccgcactaa aggctgctct agactcaccc caataaaagt taaaagtgag
 cctcaagaag atccacagtc ttacataatt taactgtgca ccagaacgaa gtgcagtact
 atttaaagaa ataacataaa atccaggccg gtggctcaca cctgtaattc cagcactttg
 ggaggctgaa gcaggtggat cacttgaggt caggagtttg agaccagcct ggccaacatg
 gtaaaacccc tctctactaa aaacacaaaa ttagcctggc gtggaggcgg gcgcttgtaa
 tcccagctac ttgggagact gaggcagaag aattgcttga acctgggagg tggaggttgc
 agtgagccga gattgcaccT GGGTGACAGA GCTAAGGTGT TTGCAGTGaa aagccaaaag
 agtttctcac cagcagacct gcattacaaa gaaccatcag ttcttcaagc agaaggaaaa
 ctttcccaga tggaaatctc aatccaggca caaaaagtga aaagacccca gaaatggtaa
 atatatgtat aaaaataaaa aatttgcttt tctgattttt aaatttcttt ttaaaagata
 attggacaaa tggtggtaca cccatagaat ggaatactac tcagcaatga aaaggaatga
 atggacttac tgatatatgc aacaacacgg ataaatcttg aaggtattat gctaagtgaa
 agacgtcaga cggaacagac tacgtattat atgattccat ttatgtaaaa ttctgtaaaa
 ggcaaaattg tagtgataga aagcagacca gtggttgcca ggggttacaa gtcaggggag
 ggtgttgact gcaaaacagg aagaggaaat tttcaggagg aatggaaaga aatgctccat
 attttgattg cagtggtggt tacactactg tatgcatttg tcaaaatgtc attgtattta
 ttgtacgctt aaattggtaa attttattgt atgtaaatta tacttcaaaa GCCAAACACA
 AATTAGTGTG AATAAGAATC GTTTGAGGAG CATGTTAAAA TGTACATCCC TGAGCCTGAC
 TCTCAGAGAA TCTATCTGAT TTGGAAGATC TGGGGTGAGG CCTAGGAATT TAAATTTTCA
 ACATGTGCCT ATTCTGAATT AAAAGATATG TCATGAAAAA Gataaattac aaaaataaag
 aaatatattt ttataaaata tGAATAAGAA AACAAAAATT GGAAGGGAAT CCTTTAAAAT
 GCCTGATGTC ATCTGGATAG CCTGGATAGC TGGATGAGAT TATGAGGGCT TTTTTTTCCC
 CCTTCTATTT TTCAACTTTA CAAAATGTTA C

  GeneView back to top
GeneView via analysis of contig annotation: NOX5 NADPH oxidase, EF-hand calcium binding domain 5
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_010194->NM_024505
svfunction
HuRefNW_001838218->NM_024505
svfunction
CeleraNW_925884->NM_024505
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010194->NM_024505->NP_07878140133907forwardintron
HuRefNW_001838218->NM_024505->NP_0787815014441reverseintron
CeleraNW_925884->NM_024505->NP_07878125330745forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs311927 maps exactly once on NCBI human chromosome 15
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
15NW_001838218.2501444146176569plusTalt_assembly_8HuRefHuRefview685
15NW_925884.12533074546232928minusAalt_assembly_1CeleraCeleraview685
15NT_010194.164013390767130642minusGref_assemblyreferencereferenceview685

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010194 AC026512 AC027088 AC027088.2
dbSNP Blast Analysis
GenBank HTGS Finished:
AC027088.8 NC_000015.8

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1896529HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 88IG 1.000 1.000
HapMap-JPTAsian 84IG 1.000 1.000
HapMap-YRISub-Saharan African 112IG 0.018 0.268 0.714 1.000 0.152 0.848
ss23415984AFD_EUR_PANELEuropean 48IG 1.000 1.000
AFD_AFR_PANELAfrican American 46IG 0.261 0.739 0.479 0.130 0.870
AFD_CHN_PANELAsian 48IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.081+/-0.18433226090

  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 .