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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs197143          
refSNP ID: rs197143
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:C
Clinical Association:unknown
HGVS Names
NM_015015.1:c.-109+19787G>A
NT_011255.14:g.4929028G>A
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 ss1631529 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs197143 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
ss259445KWOK|OVLP-000621-100183fwd/BC/Tgaaatacattttgtcctgtttcctggcctagactcccccagatcctcggaattctccagt06/30/0010/10/0379Genomic97 %
ss497715SC_JCM|AC019114.4_42796fwd/BC/Tgaaatacattttgtcctgtttcctggcctagactcccccagatcctcggaattctccagt07/12/0010/10/0387Genomicunknown
ss1255046KWOK|OVLP-000804-567545fwd/BC/Tgaaatacattttgtcctgtttcctggcctagactcccccagatcctcggaattctccagt09/02/0010/10/0386Genomic97 %
ss1631529KWOK|OVLP-000925-123662fwd/BC/Tgaaatacattttgtcctgtttcctggcctagactcccccagatcctcggaattctccagt10/04/0010/10/0387Genomic97 %
ss41042970ABI|hCV2350040rev/TA/Gactggagaattccgaggatctgggggagtctaggccaggaaacaggacaaaatgtatttc07/17/0507/17/05126Genomicunknown
ss85840725HGSV|Cor19129_SNV_20070510.chr19_4940028rev/TA/Gactggagaattccgaggatctgggggagtctaggccaggaaacaggacaaaatgtatttc12/06/0712/10/07130Genomicunknown
ss86071760HGSV|Cor18956_SNV_20070510.chr19_4940028rev/TA/Gactggagaattccgaggatctgggggagtctaggccaggaaacaggacaaaatgtatttc11/30/0712/11/07130Genomicunknown
ss90888801BCMHGSC_JDW|JWB-1138666rev/TA/Gactggagaattccgaggatctgggggagtctaggccaggaaacaggacaaaatgtatttc02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs197143|allelePos=217|totalLen=1300|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GGCAAAGAAC CAGCACTCTG CAAGCGGCTT CCACCCCAGG CCACAGGGCC CTTCACAGAG
 CACCCTGCCA AGCCCTCCAC GGCAGCGACT CACCTCTACC ACTTCAGCAC TGTCCAGACA
 GCCACCCTCC CGTCCTCTCA TCACAGACAA GGAAGCGGAG GCAAGGGACC GGCCCAGTGA
 GACTGTGAAA TACATTTTGT CCTGTTTCCT GGCCTA
 Y
 GACTCCCCCA GATCCTCGGA ATTCTCCAgt gtgctaatga ggtgactaag ggcttggcag
 cccctcggga gctgagggaa tagggctgct cactgaaaag acccaggctg gacgggaggg
 gaggggcatg tggctgaagg ctgacttgat cacccaggcc aatgcagtga ggtcacccaa
 gcctctgcga ggaagctgag gtaaaacccg gaggactggg atggaagctt ccccacagat
 gaatgcgtgg aggttcctgg agacgtcaca gcccggggag agcacggaac cctctgtgcc
 ccttcccaca tccctcaccc tacacatgtc ttcatctgcc tcctttgtaa aatcctttct
 aataagctgg taaacgtaag taacagctcc cctgagtttt gagaggtgca ttagcaaatt
 aagctcaaag aagggttcat gaggccgggc acggtggctc atgcctgtaa tcccagcact
 ttgggaagcc gaggcgggtg gatcacgagg tcaggagatt gagaccatcc tggctaacat
 ggtgaaaccc cgtctctact aaaaatacaa aaaattagcc gggcgtggtg gcgggcacct
 gtagtcccag ctactccgga ggctgaggca ggagaatggc gtgaacccag gaggcggagc
 ttgcagtgag cctagatcgc accactgcac tccagcctgg gaaacacaac aagactccgt
 ctcaaaaaag aaaaaaaaag aagggttcat gagaaggctg gtttccagcg cgtccagcag
 aagctcagga cacagcctgg ggcttgtgac tggcatgggc cgtggggtta ggtacgtggg
 gaggagcccg cagcctgtcc tgcccgatgc agcccccagg taggagtgaa ctgaacggag
 ggccccagct cctgcccctg caCCGCTTTG CTCGCGTGTG CTGGAAGGGA TCTGTGACTG
 CTCTGACAGC CTGGGAGAAA CTGAGTTTGT TATTCCCACG TTCTCAGGCC CAAGACCACA
 TCGCTGTGCA GGAAGTGGCC GAGCTGGGGG CGTGAAACCA GCTGCTGCAC CCTGGGAGTA
 GCA

  GeneView back to top
GeneView via analysis of contig annotation: JMJD2B jumonji domain containing 2B
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_011255->NM_015015
function
HuRefNW_001838477->NM_015015
function
CeleraNW_927173->NM_015015
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011255->NM_015015->NP_0558304929028forwardintron
HuRefNW_001838477->NM_015015->NP_0558301473604reverseintron
CeleraNW_927173->NM_015015->NP_0558304184942forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs197143 maps exactly once on NCBI human chromosome 19
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
19NW_001838477.214736044750638plusCalt_assembly_8HuRefHuRefview216
19NW_927173.141849424926218minusGalt_assembly_1CeleraCeleraview216
19NT_011255.1449290284940028minusGref_assemblyreferencereferenceview216

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AC019114.5 AC053467 AC053467.1
dbSNP Blast Analysis

  Population Diversity back to top
There is no frequency data.

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

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Revised: May 25, 2006 1:38 PM .