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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1071742          
refSNP ID: rs1071742
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_002116.5:c.299T>A
NM_002116.5:c.299T>C
NP_002107.3:p.V100A
NP_002107.3:p.V100E
NT_007592.14:g.20769009T>A
NT_007592.14:g.20769009T>C
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 ss20421635 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1071742 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
ss1541985LEE|819232fwd/BC/Tatgtgaaggcccactcacagactgaccgagggacctggggaccctgcgcggctactacaa09/13/0010/10/0386cDNAunknown
ss1541988LEE|819298fwd/TA/Tatgtgaaggcccactcacagactgaccgagggacctggggaccctgcgcggctactacaa09/13/0010/10/0386cDNAunknown
ss4376104SC_JCM|AL645935.6_79771rev/TA/Gttgtagtagccgcgcagggtccccaggttcctcggtcagtctgtgagtgggccttcatat02/19/0210/10/03126Genomicunknown
ss4399085LEE|ge819232fwd/BC/Tatgtgaaggcccagtcacagactgaccgaggaacctggggaccctgcgcggctactacaa04/25/0210/10/03108cDNAunknown
ss4399086LEE|ge819298fwd/BA/Tatgtgaaggcccagtcacagactgaccgaggaacctggggaccctgcgcggctactacaa04/25/0210/10/03108cDNAunknown
ss4428646LEE|e819232fwd/BC/Tatgtgaaggcccactcacagactgaccgagggacctggggaccctgcgcggctactacaa04/26/0210/10/03110cDNAunknown
ss4428649LEE|e819298fwd/TA/Tatgtgaaggcccactcacagactgaccgagggacctggggaccctgcgcggctactacaa04/26/0210/10/03110cDNAunknown
ss12681156SI_MHC_SNP|AL671277.5_20442_TCfwd/BC/Tatgtgaaggcccagtcacagactgaccgagggacctggggaccctgcgcggctactacaa09/10/0303/29/05126Genomicunknown
ss12681157SI_MHC_SNP|AL671277.5_20442_TAfwd/TA/Tatgtgaaggcccagtcacagactgaccgagggacctggggaccctgcgcggctactacaa09/10/0310/10/03126Genomicunknown
ss20421635DBMHC|HLA-A_185_226_0fwd/A/C/Tatgtgaaggcccagtcacagactgaccgagggacctggggaccctgcgcggctactacaa12/08/0601/16/08128Genomicunknown
ss24819807SEQUENOM|sqnm222662byFreqfwd/BC/Tatgtgaaggcccactcacagactgaccgagggacctggggaccctgcgcggctactacaa06/18/0408/05/04126cDNAunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1071742|allelePos=1001|totalLen=2001|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=128
 TTAAAAACAA AAACAACAAC AACAAAAATC TACACCTCCA TTCCCAGATC AAGCTTACTC
 TCTGGCACCA AACTCCATGG GGTGATTTTT CTTCTAGAAG AGTCCAGGTG GACAGGTAAG
 GAGTGGGAGT CAGGGAGTCC AGTTCAGGGA CAGAGATAAT GGGATGAAAA GTGAAAGGAG
 AGGGACGGGG CCCATGCCGA GGGTTTCTCC CTTGTTTCTC AGACAGCTCC TGGGCCAAGA
 CTCAGGGAGA CATTGAGACA GAGCGCTTCG CACAGGAGCA GAGGGGTCAG GGCGAAGTCC
 CAGGGCCCCA GGCGTGGCTC TCAGAGTCTC AGGCCCCGAA GGCGGTGTAT GGATTGGGGA
 GTCCCAGCCT TGGGGATTCC CCAACTCCGC AGTTTCTTTT CTCCCTCTCC CAACCTACGT
 AGGGTCCTTC ATCCTGGATA CTCACGACGC GGACCCAGTT CTCACTCCCA TTGGGTGTCG
 GGTTTCCAGA GAAGCCAATC AGTGTCGTCG CGGTCGCTGT TCTAAAGCCC GCACGCACCC
 ACCGGGACTC AGATTCTCCC CAGACGCCGA GGATGGCCGT CATGGCGCCC CGAACCCTCC
 TCCTGCTACT CTCGGGGGCC CTGGCCCTGA CCCAGACCTG GGCGGGTGAG TGCGGGGTCG
 GGAGGGAAAC CGCCTCTGCG GGGAGAAGCA AGGGGCCCTC CTGGCGGGGG CGCAGGACCG
 GGGGAGCCGC GCCGGGACGA GGGTCGGGCA GGTCTCAGCC ACTGCTCGCC CCCAGGCTCC
 CACTCCATGA GGTATTTCTT CACATCCGTG TCCCGGCCCG GCCGCGGGGA GCCCCGCTTC
 ATCGCCGTGG GCTACGTGGA CGACACGCAG TTCGTGCGGT TCGACAGCGA CGCCGCGAGC
 CAGAGGATGG AGCCGCGGGC GCCGTGGATA GAGCAGGAGG GGCCGGAGTA TTGGGACCAG
 GAGACACGGA ATGTGAAGGC CCAGTCACAG ACTGACCGAG
 H
 GGACCTGGGG ACCCTGCGCG GCTACTACAA CCAGAGCGAG GCCGGTGAGT GACCCCGGCC
 GGGGGCGCAG GTCAGGACCC CTCATCCCCC ACGGACGGGC CAGGTCGCCC ACAGTCTCCG
 GGTCCGAGAT CCACCCCGAA GCCGCGGGAC CCCGAGACCC TTGCCCCGGG AGAGGCCCAG
 GCGCCTTTAC CCGGTTTCAT TTTCAGTTTA GGCCAAAAAT CCCCCCGGGT TGGTCGGGGC
 TGGGCGGGGC TCGGGGGACT GGGCTGACCG CGGGGTCGGG GCCAGGTTCT CACACCATCC
 AGATAATGTA TGGCTGCGAC GTGGGGTCGG ACGGGCGCTT CCTCCGCGGG TACCGGCAGG
 ACGCCTACGA CGGCAAGGAT TACATCGCCC TGAACGAGGA CCTGCGCTCT TGGACCGCGG
 CGGACATGGC GGCTCAGATC ACCAAGCGCA AGTGGGAGGC GGCCCATGAG GCGGAGCAGT
 TGAGAGCCTA CCTGGATGGC ACGTGCGTGG AGTGGCTCCG CAGATACCTG GAGAACGGGA
 AGGAGACGCT GCAGCGCACG GGTACCAGGG GCCACGGGGC GCCTCCCTGA TCGCCTGTAG
 ATCTCCCGGG CTGGCCTCCC ACAAGGAGGG GAGACAATTG GGACCAACAC TAGAATATCA
 CCCTCCCTCT GGTCCTGAGG GAGAGGAATC CTCCTGGGTT CCAGATCCTG TACCAGAGAG
 TGACTCTGAG GTTCCGCCCT GCTCTCTGAC ACAATTAAGG GATAAAATCT CTGAAGGAGT
 GACGGGAAGA CGATCCCTCG AATACTGATG AGTGGTTCCC TTTGACACCG GCAGCAGCCT
 TGGGCCCGTG ACTTTTCCTC TCAGGCCTTG TTCTCTGCTT CACACTCAAT GTGTGTGGGG
 GTCTGAGTCC AGCACTTCTG AGTCCCTCAG CCTCCACTCA GGTCAGGACC AGAAGTCGCT
 GTTCCCTTCT CAGGGAATAG AAGATTATCC CAGGTGCCTG

  GeneView back to top
GeneView via analysis of contig annotation: LOC100133382 hypothetical protein LOC100133382
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: HLA-A major histocompatibility complex, class I, A
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
c6_QBLNT_113893->XM_001713644
svfunction
referenceNT_007592->NM_002116
svfunction
c6_COXNT_113891->NM_002116
svfunction
HuRefNW_001838980->NM_002116
svfunction
CeleraNW_923073->XM_001713645
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
c6_QBLNT_113893->XM_001713644->XP_001713696522327forward307missenseAGlu [E]2100
missenseTVal [V]2100
contig referenceCAla [A]2100
referenceNT_007592->NM_002116->NP_00210720769010forward299missenseAGlu [E]2100
missenseCAla [A]2100
contig referenceTVal [V]2100
c6_COXNT_113891->NM_002116->NP_0021071359017forward299missenseAGlu [E]2100
missenseTVal [V]2100
contig referenceCAla [A]2100
HuRefNW_001838980->NM_002116->NP_0021072981553forward307missenseAGlu [E]2100
missenseCAla [A]2100
contig referenceTVal [V]2100
CeleraNW_923073->XM_001713645->XP_0017136972973292forward307missenseAGlu [E]2100
missenseTVal [V]2100
contig referenceCAla [A]2100

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1071742 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_001838980.1298155329709244plusTalt_assembly_8HuRefHuRefview1000
6NT_007592.142076901030018738plusTref_assemblyreferencereferenceview1000
6NT_113893.152232730042993plusCalt_assembly_4c6_QBLc6_QBLview1000
6NT_113891.1135901730047560plusCalt_assembly_3c6_COXc6_COXview1000
6NW_923073.1297329231508971plusCalt_assembly_1CeleraCeleraview1000

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm222662 M64740 AB023056 Hs.181244
dbSNP Blast Analysis
GenBank HTGS Finished:
AB023056.1 AL671277.5 NC_000006.10

dbMHC locus: HLA-A
  Population Diversity back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceHWPC
T
ss24819807CEPH 184AF 0.740 0.260

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.385+/-0.2110000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .