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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1883938          
refSNP ID: rs1883938
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:92/129
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
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 ss12489659 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1883938 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
ss2763197TSC-CSHL|TSC0899143byFreqfwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag01/02/0104/07/0492Genomicunknown
ss5757360SC_JCM|NT_011387.7_18299660fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag01/10/0310/10/03111Genomicunknown
ss8355964SC_SNP|NT_011387.8_18301603fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag04/17/0310/10/03114Genomicunknown
ss12489659WI_SSAHASNP|chr20.NT_011387.8_18301603byFreqfwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag07/04/0305/16/04116Genomicunknown
ss20125961CSHL-HAPMAP|CSHL-HuFF-200402.chr20.NT_011387.8_18301603fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag02/21/0403/04/04120Genomicunknown
ss21775187SSAHASNP|WGSA-200403-chr20.chr20.NT_011387.8_18301603fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag03/20/0403/20/04121Genomicunknown
ss28511295MGC_GENOME_DIFF|BC033985x27501067-T18301603Cfwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag08/25/0408/25/04126cDNAunknown
ss65725980ILLUMINA|Human1-rs1883938fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag10/10/0610/10/06127Genomicunknown
ss66641619ILLUMINA|HumanHap300v1.1_rs1883938fwd/TC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag11/09/0611/09/06127Genomicunknown
ss67203142ILLUMINA|HumanHap550v1.1_rs1883938fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag11/14/0611/14/06127Genomicunknown
ss67595270ILLUMINA|HumanHap650Yv1.0_rs1883938fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag11/14/0611/14/06127Genomicunknown
ss69238444PERLEGEN|PGP07859423byFreqfwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag01/30/0708/14/07127Genomicunknown
ss70681368ILLUMINA|HumanHap550v3.0__rs1883938fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag04/20/0703/30/08130Genomicunknown
ss71245113ILLUMINA|HumanHap650Yv3.0_rs1883938fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag04/23/0704/23/07127Genomicunknown
ss75497089ILLUMINA|ILMN_Human_1M_rs1883938fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag08/28/0708/29/07129Genomicunknown
ss78442081HGSV|Cor12878_SNV_20070510.chr20_18309603fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag10/17/0710/19/07129Genomicunknown
ss79098646ILLUMINA|HumanHap300v2.0_rs1883938fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag04/18/0711/18/07130Genomicunknown
ss83901657KRIBB_YJKIM|KHS568685fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag12/04/0712/06/07130Genomicunknown
ss91658417BCMHGSC_JDW|JWB-1427528fwd/BC/Tctgaagcccactggggacataggacaagtcgcaaagcagagacagcccctccaggaagag02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1883938|allelePos=1917|totalLen=2117|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 Tatgctgtag ccaaccccca tgtgcaggta gggggcattt aaaatgtggt gaattgaatt
 aagatgtgct gtaaggataa aatgcacacc agatttcaat gacttggtgt gaaaaaataa
 cataaaatat atagaatatt gcattaacaa tttagatgaa ttataaattg aaataataTT
 TATTCTAGTA AAATAttttt aaaactttta ttttcggttc agggtttgtt atataggtaa
 actcatatca tgggggttta ttgtacagat tattttgtta cccaggtact aagcctagta
 cccaatcgtt attttttctg atcctctccc tcctcccagc ctccaccttc tgagaggccc
 cagtgggtgt tttcccccca cctgtttttt tttttttttg agacagagtc tcactctgtc
 gcccaggctg gagtgcagtg gggatctcag ctcactgcaa gctctgcctc ccaggttcat
 gccattctcc tgcctcagcc tcccgagtag ctgggactac aggtgcccgc caccacgccc
 agctaatttt ttgtattttt ttagtaggga cggggtttca ccatgttagc caggatggtc
 tcgatctcct gacttcgtga tctgcccgcc tcggcctccc aaagtgctgg gattacaggc
 gtgagccacc gcgcctggcc ggtgttgtcc ctctttttgt gtccatttgt tctcatcatt
 tagctgccac tttttttttt tttttttttg gacatggagt ttcactctcg tcgcccaggc
 tggagtgcaa cggcaagatc ttggctcact gcaacctctg cctcctgggt tcaagcaatt
 ctgcctcagc ctcccgagta gctgggacta caggcgccca ctaccaggcc gggctaattt
 ttgtattttc agtagagatg aagtttcact atgttggcca ggctagtctc caactcctga
 cctcaggtga tctgcctacc ttggcctccc aaagtgctgg gattacaggc gtgaaccacc
 gtgcctggcc agctcccacg tataagtgag aacatgtgat atttggtttt ctgttcctgt
 gtttgtttgc taaggataat ggcctctagc tccatccgtg ttcccacaac agacatgttc
 ttgttctttc ttatggctgc atagtctatt tcatggtgta tatgtaccac attttcttta
 tccaatctgt cattgatggg catttaggtt gtttccatgt cttttctatt gtgaatagtg
 ctgcaatgaa catacacatg catgggtctt tatggtagaa tgatttatat tcctttgggt
 gtatacccaa taatgagatt gctgggttga atggtatttc tatttttagc tctttcagga
 atcaccatac tgttttccac aacggttaaa cactcccacc aacagggtat aagcatcccc
 ttttttccac aaccttgcca gcatgttatt ttttgacttt ttaaaaatag ccattctgat
 tggtgttaga tggtatctca ttgtggtttt gatttccatt tctctaatga ttagtgacac
 cgagcttttt ctttttttca tatgctttct ggccacaagt atgtcttctt tggaaaagta
 tctgtccatg tATCCCAGta aaattaattt tgcttgtttc tctgcacttt tagaagtatg
 gctactagaa aatttatgat tgtatatgtg gctcagattg tatttctatt ggacagcact
 gTCTGGACTC TAGAAGATGC TCTGATTCAA GAGGATGTAA AGAAATTCTC TAAGCCGATA
 AGAAAAATAG AAGAAACCCA AATGGGCAAT GAGTGCATGG GAACTCACTC ACCTCAGTGG
 AAAGGAGGGA ATGGCAAGCC AGCCCACTGA AGCCCACTGG GGACATAGGA CAAGTC
 Y
 GCAAAGCAGA GACAGCCCCT CCAGGAAGAG CGACCAGGCC TTGAGAGGAC ATGGCCTTAG
 GACCAGATCC AGGGAAGACA CAGTCACTAA CCCCTGGCTC ATCTGGCAGG TGTGGGAAGC
 AGCCAGGCCC GTGGCTTCAC CAGCTCCCCC CGATCTCTGC CTTCAGCTGT CCTGCAGCCT
 GGGTCAGGCA CCTAGGCAGC

  GeneView back to top
GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1883938 maps exactly once on NCBI human chromosome 20
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
20NT_011387.81830160318309603plusTref_assemblyreferencereferenceview1916
20NW_001838652.11832372918323729plusCalt_assembly_8HuRefHuRefview1916
20NW_927317.11829286818435692plusCalt_assembly_1CeleraCeleraview1916

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011387.7 BC033985
dbSNP Blast Analysis
GenBank HTGS Finished:
AL049646.19 NC_000020.9
UniGene Cluster ID
120399

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss12489659CEPH 184AF 0.940 0.060
HapMap-CEUEuropean 120IG 0.867 0.117 0.017 0.251 0.925 0.075
HapMap-HCBAsian 84IG 0.738 0.262 0.343 0.869 0.131
HapMap-JPTAsian 86IG 0.767 0.233 0.403 0.884 0.116
HapMap-YRISub-Saharan African 120IG 0.467 0.483 0.050 0.200 0.708 0.292
ss2763197AfAmAfrican American 18IG 0.778 0.222 0.752 0.889 0.111
CaucasianEuropean 40IG 0.750 0.250 0.527 0.875 0.125
AsianAsian 30IG 0.867 0.133 1.000 0.933 0.067
CEPHEuropean 28IG 0.500 0.500 0.251 0.750 0.250
PDpanelGlobal 46IG 0.783 0.174 0.043 0.273 0.870 0.130
ss69238444HapMap-CEUEuropean 120GF 0.867 0.117 0.017 0.925 0.075
HapMap-HCBAsian 90GF 0.756 0.244 0.878 0.122
HapMap-JPTAsian 90GF 0.778 0.222 0.889 0.111
HapMap-YRISub-Saharan African 120GF 0.483 0.467 0.050 0.717 0.283
Concordant GenotypeTotal SampleC/CC/TT/T
ss12489659268186707
ss27631978362201
ss69238444268191707
RefSNP Genotype SummaryTotal IndividualC/CC/TT/T
rs1883938350250908
Discordant Genotypes:
Indiviudal
SampleID		SubSNP(ss)GenotypePopulation
Handle		Submitter
Population		Submitter
SampleID		SampleID
Alias		Submission
Batch		NCBI
ProbeID
5144ss12489659C/TCSHL-HAPMAPHapMap-YRINA19192YOR112.03r23_ch20_YRI_illumina:golden_gate_1.0.0916135
5144ss69238444C/CCSHL-HAPMAPHapMap-YRINA19192YOR112.03chr20-HapMap-YRI
5307ss12489659C/TCSHL-HAPMAPHapMap-YRINA19145YOR074.01r23_ch20_YRI_illumina:golden_gate_1.0.0916135
5307ss69238444C/CCSHL-HAPMAPHapMap-YRINA19145YOR074.01chr20-HapMap-YRI
Genotype data submitted for353 samples from350 individualsIndividual with multiple genotypes submission:270

  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, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .