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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs195754          
refSNP ID: rs195754
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:A/T
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_017772.2:c.982+8679A>T
NT_007592.14:g.28126062A>T
Links

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 ss1839207 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs195754 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
ss257726KWOK|OVLP-000621-90785rev/BA/Taagagtattagaagaaaacacgggagagtattttgtaatctttttttttttttttttttg06/30/0010/10/0379Genomic97 %
ss1032684KWOK|OVLP-000804-431311fwd/TA/Tcaaaaaaaaaaaaaaaaaaagattacaaaatactctcccgtgttttcttctaatactctt09/02/0010/10/0386Genomic97 %
ss1839207KWOK|OVLP-000925-624139byFreqfwd/TA/Tcaaaaaaaaaaaaaaaaaaagattacaaaatactctcccgtgttttcttctaatactctt10/05/0010/25/0687Genomic97 %
ss10338477BCM_SSAHASNP|chr6.NT_007592.13_28064939fwd/TA/Tcaaaaaaaaaaaaaaaaaaagattacaaaatactctcccgtgttttcttctaatactctt06/29/0310/10/03116Genomicunknown
ss22496072SSAHASNP|WGSA-200403-chr6.chr6.NT_007592.13_28064939fwd/TA/Tcaaaaaaaaaaaaaaaaaaagattacaaaatactctcccgtgttttcttctaatactctt03/21/0403/21/04121Genomicunknown
ss77171014HGSV|Cor12156_SNV_20070510.chr6_37375790fwd/A/Tcaaaaaaaaaaaaaaaaaaagattacaaaatactctcccgtgttttcttctaatactctt10/09/0710/11/07129Genomicunknown
ss93443925BCMHGSC_JDW|JWB-2126569fwd/A/Tcaaaaaaaaaaaaaaaaaaagattacaaaatactctcccgtgttttcttctaatactctt02/26/0803/04/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs195754|allelePos=1601|totalLen=2340|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 ATATAGATCC ACTTCATTAT TTTCAGCAAT TCCATTATTT CTATAACAAG ACTTAACTAT
 AGTTTAACTT TTCTTCTCTA GAAGAACATT TAAGTTGCCT ACAGtttttt tttttttttt
 ttttttttga gacggagtct tgctctgttg cccaagccgg agtgcagtgg cgcgatctcg
 gctcactgca agctccgcct cccgggttca cgccattctc ttgcctcagc ctcccgatta
 gctgggacta caggcgcccg ccaccacgca cagctaattt tttgtatttt taggaaagac
 ggggtttcac catgttagcc aggatggtct cgatctcctg acctcgtgat ccgcccacct
 cggcctccca gagtgttggg attacaggcg tgagccaccg cgcctggcct aagttgccta
 cagtttttag ctgttataag taacattgca gtgaatatcc ttgtacatat tttcttgtgc
 acttgttaaa atatgtattt ctctgaaaga gtcctagaag tgaaattact aatcctgaaa
 gcatgccaaa taggtactac tgaattataa tccaaaaatg tttataccag tttgtactcc
 agccatgaaa tgtgtggatg cacttttcct cacctcctta gcaaaacctg tgtatggatg
 aagtctagtg tatttcacct gtctagcaga taaaccatgg tttgtgtttc agtttttgtt
 tccactttct ggtcagtgat attatgtatc ttttctcatc tgtattatca ttttcttttg
 tggtctgctg gtttaatcat ttacctattt tttctaatgg attattgacc tgtcttgttt
 tgtaagagct ttttgtatat tAGATAAATT TATCCTTCAT CTGCTATGTG TTAAAAATAT
 TAGGTTGAAT CATATAAATT GTTAATACTC AACCTTTTTT TTACCGCCCA ACATGGGAAT
 TTTATGTAGT CCAACCTAAT ATTTTCCCCA GACCATTATT TATCTCTTAA CTTTGCTACT
 TGTGTCTCTT TATGTAGAAC TTAGTAATTT TTATACAGTC AGatctgtcc attcaacaag
 tatttattaa gctgttacta tgtgccaggA GATAGACATG GGCCTGCCCT TGTGGCAACT
 CCTGTCTGGT AGGGAGGCTC ACAAACAAGT CACCAGATAA TTGCAAACTG TGATGAAGCC
 TCTGAGGGAA GCAGCTTCTC CTTTAGGGTT TTTGGATTTG GTATCTTGCT TAGGAACTCT
 TTCCTTCCCC ACCTCAAGAT TACAAAAATA CTggccgggc atggtggctc acatctgtaa
 tcccagcact ttgggaggct gagacaggcg gatcacatga gatcaggagt tccagaccaa
 tttggtcaac atggcaaaac ccgtctctac caaaaataca caaattagcc gggcatggtg
 gcggctgcct gttatctcag ctactcggga ggctgaggca ggagaatcgc ttgaacctgg
 gaggcagagg ttgcagtgag ccgagatcac gccactgcac tctagcctgg gtgacagagt
 gagactctgt caaaaaaaaa aaaaaaaaaa gattacaaaa
 W
 tactctcccg tgttttcttc taatactctt gtggctttaa catttaactt tttaaattcc
 attactaatt tattttcttg tatgatgaga actgagattt atagttacta ttccagttgc
 atagctaatt atttcgacac catttataaa taatacacca tcttttcacc GATGTGAAAT
 CTCTCTTCAT AATATTACGT AATTTTAATT ACATGGTTCT GCTGCTTTGT TGGTTTGATT
 TTATTTGTCT CCATTTCTAT CCAGTACCAC ACAGCTTAGA TTTTTTGAGT TTATAAAGTT
 Gttaaattat tattattata tattttattt atttatttat tttgagatgg aatctcactc
 tgttgcctag gctggagtgc aatggcacaa tcttggctca ctgcaacttt catctcccag
 gttcaagcca tcctcccacc tcagcctccc tagtagctgg aactacaggc atcgccacta
 tgcctggcta atttttgtat ttttgagtag agacggggtt ttaccacgct ggccaggctg
 gtctggaact cctggcctga agtcctccac ccaccttggc ctcccaaaac accgggatta
 caggcatgag ccaccgtgcc tggctattat tttttattaG TGGCTTTTTA AAAAAAATTC
 CCCCCACCCA GGGCCAGTCT CTTTCATTAT CCTTTAAAAA AATACTGTCT TGGTTGTTCT
 TCCAGATGAA CTTATTTTT

  GeneView back to top
GeneView via analysis of contig annotation: TBC1D22B TBC1 domain family, member 22B
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_007592->NM_017772
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_007592->NM_017772->NP_06024228126062forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs195754 maps exactly once on NCBI human chromosome 6
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
6NW_001838980.11025904236986733plusTalt_assembly_8HuRefHuRefview1600
6NT_007592.142812606237375790plusAref_assemblyreferencereferenceview1600
6NW_923073.11028712338822802plusTalt_assembly_1CeleraCeleraview1600

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007592 AL096712.20
dbSNP Blast Analysis
GenBank HTGS Finished:
AL096712.20

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/T
T/T
HWPA
T
ss1839207HapMap-CEUEuropean 120IG 0.233 0.767 0.317 0.117 0.883
HapMap-HCBAsian 90IG 0.111 0.889 0.752 0.056 0.944
HapMap-JPTAsian 90IG 0.067 0.933 0.033 0.967
HapMap-YRISub-Saharan African 118IG 0.051 0.458 0.492 0.317 0.280 0.720

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.229+/-0.24927021000

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

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Revised: May 25, 2006 1:38 PM .