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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1860187          
refSNP ID: rs1860187
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 ss43981016 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1860187 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
ss2733982TSC-CSHL|TSC0849143fwd/BC/Ttggtttctggtttcctttgtgagttccctcttttccattattcccctttggtcacctctg01/02/0110/25/0692Genomicunknown
ss6190403SC_JCM|NT_010799.10_2214900rev/TA/Gcagaggtgaccaaaggggaataatggaaaagagggaactcacaaaggaaaccagaaacca01/10/0310/10/03111Genomicunknown
ss16360931FHCRC|ABF132_2274byFreqrev/TA/Gcagaggtgaccaaaggggaataatggaaaagagggaactcacaaaggaaaccagaaacca01/28/0404/07/04120Genomicunknown
ss16738440CSHL-HAPMAP|CSHL-HuAA-200402.chr17.NT_010799.14_7339190byFreqrev/TA/Gcagaggtgaccaaaggggaataatggaaaagagggaactcacaaaggaaaccagaaacca02/17/0405/16/04120Genomicunknown
ss43981016ABI|hCV2590331byFreqrev/TA/Gcagaggtgaccaaaggggaataatggaaaagagggaactcacaaaggaaaccagaaacca07/18/0511/03/06126Genomicunknown
ss66673930ILLUMINA|HumanHap300v1.1_rs1860187fwd/BC/Ttggtttctggtttcctttgtgagttccctcttttccattattcccctttggtcacctctg11/09/0611/09/06127Genomicunknown
ss67199940ILLUMINA|HumanHap550v1.1_rs1860187fwd/BC/Ttggtttctggtttcctttgtgagttccctcttttccattattcccctttggtcacctctg11/14/0611/14/06127Genomicunknown
ss67591697ILLUMINA|HumanHap650Yv1.0_rs1860187fwd/BC/Ttggtttctggtttcctttgtgagttccctcttttccattattcccctttggtcacctctg11/14/0611/14/06127Genomicunknown
ss70678162ILLUMINA|HumanHap550v3.0__rs1860187rev/TA/Gcagaggtgaccaaaggggaataatggaaaagagggaactcacaaaggaaaccagaaacca04/20/0703/30/08130Genomicunknown
ss71241539ILLUMINA|HumanHap650Yv3.0_rs1860187fwd/BC/Ttggtttctggtttcctttgtgagttccctcttttccattattcccctttggtcacctctg04/23/0704/23/07127Genomicunknown
ss75576094ILLUMINA|ILMN_Human_1M_rs1860187fwd/BC/Ttggtttctggtttcctttgtgagttccctcttttccattattcccctttggtcacctctg08/28/0708/29/07129Genomicunknown
ss79096328ILLUMINA|HumanHap300v2.0_rs1860187fwd/BC/Ttggtttctggtttcctttgtgagttccctcttttccattattcccctttggtcacctctg04/18/0711/18/07130Genomicunknown
ss83888603KRIBB_YJKIM|KHS565606fwd/BC/Ttggtttctggtttcctttgtgagttccctcttttccattattcccctttggtcacctctg12/04/0712/06/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1860187|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TAAAAGTCTG CCATCCAGAA CATCACACAC CGGGGCCTTT TGGAGGGTGG GGGGCTGGGG
 GAGGGATAGC ATTAGGAGAA ATACCTACAG TAAATGACAA GCTGATGAGT GCAGCAAACC
 AACATGGCAC ATGTATACCT ATGTAACAAA CCTGCACGTT GTGCACACAC ACCCGAGAAC
 TTAAAGTATA ATAAAAAGAA AAAAAAAGTC CCCCATCCTT GATTAGACTG GTTCTCTCTT
 TCTGGGGGAG CTCTGTTGTC TTGTTGATCC TGGTTTCTGG TTTCCTTTGT GAGTTCCCTC
 Y
 TTTTCCATTA TTCCCCTTTG GTCACCTCTG AAGTGAGTAT TGAAGAGAGA CATGCTCTTC
 TTGGGGGCTC TGCTGTCTTT GAGGACTGCA AGCTGTACAG CAAGGCCTGG AGTTTGTCTT
 CTTTTTGAAC TTGTCAGGAC CACTCATGGT TTCACTGACA ATATAGTACA GCTCTGGTAA
 TAACAGTGGG CTTCTGATAT CTTCACTCTC AGTCAATTCC ATATGCCAGC AGCCACAGCC
 CAAGTTTCTT TCTTGGTATA ATTTTCCAAT TATTTTTCCT CTCTCTCTCT CCCTCTCCCT

  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:  rs1860187 maps exactly once on NCBI human chromosome 17
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
17NW_001838432.126314228787515minusGalt_assembly_8HuRefHuRefview300
17NW_926772.1359060729512023minusGalt_assembly_1CeleraCeleraview300
17NT_010799.14733919029626323minusGref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010799.10
dbSNP Blast Analysis
GenBank HTGS Finished:
AC005549.1 NC_000017.9

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss16360931POPU1 40AF 0.925 0.075
ss16738440CEPH 184AF 0.850 0.150
ss43981016HapMap-CEUEuropean 120IG 0.833 0.150 0.017 0.479 0.908 0.092
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.051+/-0.15227021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: ILLUMINA
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .