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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs197140          
refSNP ID: rs197140
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/C
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_015015.1:c.-109+22176T>G
NT_011255.14:g.4931417T>G
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 ss1631526 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs197140 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
ss259442KWOK|OVLP-000621-100179fwd/TA/Ctcactgtgttgcccaggctggtctcgaactctggactcaagtgatcctcccacctctgcc06/30/0010/10/0379Genomic97 %
ss845383SC_JCM|AC053467.1_34124rev/BG/Tggcagaggtgggaggatcacttgagtccagagttcgagaccagcctgggcaacacagtga07/27/0010/10/0387Genomicunknown
ss1255043KWOK|OVLP-000804-567542fwd/TA/Ctcactgtgttgcccaggctggtctcgaactctggactcaagtgatcctcccacctctgcc09/02/0010/10/0386Genomic97 %
ss1631526KWOK|OVLP-000925-123659fwd/TA/Ctcactgtgttgcccaggctggtctcgaactctggactcaagtgatcctcccacctctgcc10/04/0010/10/0387Genomic97 %
ss10940543BCM_SSAHASNP|chr19.NT_011255.13_4931417rev/BG/Tggcagaggtgggaggatcacttgagtccagagttcgagaccagcctgggcaacacagtga06/30/0310/10/03116Genomicunknown
ss78932005HGSV|Cor18507_SNV_20070510.chr19_4942417rev/BG/Tggcagaggtgggaggatcacttgagtccagagttcgagaccagcctgggcaacacagtga10/19/0710/21/07129Genomicunknown
ss85275014HGSV|Cor19129_SNV_20070510.chr19_4942417rev/BG/Tggcagaggtgggaggatcacttgagtccagagttcgagaccagcctgggcaacacagtga12/06/0712/08/07130Genomicunknown
ss90888810BCMHGSC_JDW|JWB-1138669rev/BG/Tggcagaggtgggaggatcacttgagtccagagttcgagaccagcctgggcaacacagtga02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs197140|allelePos=3619|totalLen=4317|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 TCCTTGAAAA CCCAAGCCAT TGAACTGATT AAGTGAAATC CTGATTGCTA AGCACAGTTC
 AAAAGGAGTA AGCACAGCCT TGCTTCAAAT GATATTGGGG ATCTGAAGTC GATTCTGAGA
 AGTTAAGATG CCTATAAGAC CGACAGCAAC TACTAAGAAA ATACTTCCAA AAATATAGTG
 Ctaacaatca tgaaaagaat taaaatatta cactagaaaa tattcactta atgcaaaaga
 aaacatcaaa gaaggaataa aggaacaaaa tagaaaacaa aaagggaaat ggcaggtaca
 aatccaacta tatcaataac ggcattaaat atgaatggat taaacatcca atcaaaagac
 agaaattgtc agactggatt taaaaaacaa gatccaacta tatactatac tatatactgt
 cttcagggga cacttttttt tttttttttt tttttttttg agagacagag tttcactctt
 gttgcccagg ctggagtgca atggcatgat cttggctcac tgcaatctcc acctcccggg
 ttcaagcgat tctcctgcct cagcctcctg agtagctggg actacaggca tgcgccacca
 cgcatgtgta tttttagtag agacaaggtt tctccatgtt ggtcagcctg gtctcaaact
 cccaacctca ggtgatccac ccgcctcggc ctcccaaagt gctgagatta caggcgtgag
 ccactgcgcc cagccagggg acactcttta gattcaaaga tacgaacagg ctgaaaatag
 gctgggcaca gtggctcaca cctgtaatcc caacacttcg ggaggcctag gcaggcaaac
 tgcttgagcc caggagttcg agatcagctt aggcaatgtg gcaaaacccg tctctacaga
 aaaaacacaa aaattagcca ggtatggtgg tgcatgccGG GAGGTCGAAA CCCTGTCTCA
 AAAAAGACAA AACAACAATA ACAAAAAaaa aaaaaaaaaa aaaacaggct gaaaatataa
 aaattaaacg tgtaacatgc aaacaggaac cataagaaag ctggagtggc tacactaaca
 tcagacaaaa tagacttaaa aaaaaatgtg ccaggtgtgg tataatgact catgcctgta
 atccaagcac ttcaggaggc caaggtggga ggatcacttg agttcaggag tttgacacca
 gcctgggcaa catagtaaga cctcacctct gttaaaattc aaaaaaatta gccaggcgtg
 gcaacacaca cctgtagtcc cagctactta ggatgctgag gcaggaggat tacttgagcc
 caggaggctg aggctgcaat gagccatgat cgcaacactg cactccagac tgggcaaaag
 tgcaagactc catctcaaaa aaaaaacaaa caaaaaagtt actagagata aagagggaca
 ttttataatg ataaaaaggt gaatccatta gcaagataca gcaattataa acatatatgc
 atctaataac agagccccaa aatacatgaa gcaaaaaatg acagaaataa aaggagaagt
 aattcaacaa tagctggaga tgtcaatacc ttcactttct tttttttttt tcccttgaga
 tggagtctca ctctgtcgcc caggctggag ggtagtgggg tgatctcagc tcactgcaac
 ctctgcctcc cgggttcaag cgattctggt gcctcagcct cccgagtagc tggaatacag
 gcatgcgcca ccacactcgg ctaatttttg tgtttttagt agagacaggg ttttgccttg
 ttggccaggc tggtctcaaa ctgctgacct caggtgatcc actcacctcg gcctcccaaa
 gtgctgagat tacaggcatg agcccccatg cccggctcat accctcactt tcaataaaag
 ataacacaac tagcagaaga gcaacaaaga gagagacttg agcactataa gccaaaagaa
 tctatagaac atattctctt ctcagtacat atggaacatt ctccaggata aaccatatgt
 tagtccataa aacaagcctc attaaattga aaagaattca gatcatccaa agtaagttct
 ccaaccacaa tggaaattag aaatcaacaa cagaaagtaa tttggggatt cacaagtaca
 tggaaattaa ccaacatact cctaaataat cacagggttg aacaggaaga aaatattaga
 aaatattttg aggtgaatga aaatgaactc acaacaaagt aaaacttata ggatggccag
 acacagtggc tcatgcctgt aatcccagca ctttgggagg ccaaggtgag aggaatgctt
 gaacccagga gtacgagacc agcctgggga aatatagtga gacctcctct ccacaaaatt
 attttttaaa ttagccaggg atagtagcac atgcctctgg tcccagctac ttggtgggct
 gaggtgggag gattgcttga gctcgggagg tcaaggctgc agtgatttgt gactgcacca
 ctgcactcca gtctgggcaa cagagcaaga tcctatcgca aggaaaaaaa aaaagtacag
 gttgcagcta aagcagtact tagagggaaa tttataattg cctatacagt ttttaaaaag
 aggaagatct caaatattaa tttaagcatc tcccttaaga cactggaaaa agaagagcac
 acggaaacta aggcagatgg agcacagtac gtaacaaaga taacgagcaa aaataaacaa
 aatagagaca gccaatgaaa ccaaaagtcg gtcccttgaa aagaccagta aaactgTCGA
 AGGTAAATGT CTTCGTGACA TTTTGTTATC TGCACAGATT CCTGGAACCG CCACTGCAAT
 CAGATACAGG GCTGTTCCGT CAACACAAAG GAACTCACTC TGCTTCCACT CTGTCGCCCC
 CAGGCCCTGG CAACCTTGGA TCTTGTCCTC CATCTCTGGA GAACTCAAAT TGCTAAAATC
 GGGAATGAAA GATGGGACCT TACCACTGCC ACCCGTCTCA CAGAAATAAG CAGAATGAGA
 AAACAACACC CGTatggaga actactgagt aataaaagaa agtaactact gatacacaca
 acaacttcga cagattgcaa gcgaaaaaac ccaatcccaa gaggttaaat acgctgtgat
 tccatctaca taacattctc aaaagggcaa ggttacagag atgcagagat cctcagccgt
 cgccagggcc tgggggtgac agaagggaga agcagagcgt tcctttgtgt tgacagaaca
 gttctgtatc ttgattgcaa tggtggttcc tggaatctgt gcaggtaaca gaatgtcgca
 aagactctac caaaagaatg agccagtgct aacactgagg acgcctgagg aaggtctgaa
 gccacagtgt cctgtgtcaa tttcctagtt ttaacgggac actaaagtta tgtaaaatgt
 taccactgga gacagcaggg tgaagcctag ggaaatctct ttattatttt tgcaacacct
 tggcagtcta taattCATTC TTatttttgc ttttgtagcg acagggtctc actgtgttgc
 ccaggctggt ctcgaact
 M
 ctggactcaa gtgatcctcc cacctctgcc tcccaaagtg cctggatgac aggtgtgagc
 caccacaccc agccTCTGTA ATTCTTTAAA AATTAAAAGT TAACAAAAAT AATATGAGGG
 CTATTTCACC ACAGATGGGG GTAGGGCAGG GGGGGTTGCC ATGGGTTGAT GGTTTTGGGG
 CTGGGTGAGG GGCCTGGGGG GCTCGTTATT CCATGTTGTC TACCTTTCTG TGTAGTCAAA
 TTCTCCATAA CAGTGttttt atttttattt tttgctttac tattttttga gaccgagtct
 cactctgtcg cccaggcagg agtgcagcgg cacaatctca gctcactgca tcctccgcct
 cctgggttca agcaattctc ctgtcccctc cctagtagct gggactacag gcgcccgcca
 tcacgcccag ctaatttttg tatttttagt aaagacgagg tttcaccata ttggtcaggc
 tggtctcgaa ctcctgatct caggtggtcc gcccacctca gactcccaaa gtgctgggat
 tataggcgtg agccatcata cccggccCat aataaagttt tttaaaaaaa ataataaaGG
 GAACCAACAC AAGAATAGCA CTAAGAAGGG CCTTATCCAT CCGGGTTTAT AAATATCCTT
 CAAAATGCAC AGTGTTAGAA TTACGGGCCA TCTCATCG

  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_0558304931417forwardintron
HuRefNW_001838477->NM_015015->NP_0558301471215reverseintron
CeleraNW_927173->NM_015015->NP_0558304187331forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs197140 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_001838477.214712154753027plusAalt_assembly_8HuRefHuRefview3618
19NW_927173.141873314928607minusTalt_assembly_1CeleraCeleraview3618
19NT_011255.1449314174942417minusTref_assemblyreferencereferenceview3618

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011255 AC019114 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
byClusterwith2hit
DoubleHit found by:  BCM_SSAHASNP, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .