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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs3187686          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:105/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_001015050.1:c.550G>A
NP_001015050.1:p.Gly184Ser
NR_024250.1:c.1285C>T
NR_024251.1:c.1383C>T
NT_005612.15:g.32143355C>T
XR_037841.1:c.934G>A
XR_040853.1:c.1668C>T
XR_041463.1:c.1760T>C
XR_041464.1:c.1763C>T
XR_041465.1:c.1759C>T
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 ss42077750 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3187686 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
ss4411826LEE|e282694fwd/BC/Tcactgggaggtgctgctcgaaagggtttgcctgagactccaagaagaagctgcgggaagg04/26/0210/10/03105cDNAunknown
ss4998085YUSUKE|IMS-JST171609byFreqfwd/BC/Tcactgggaggcgctgctcaaaagggtttgcctgagactccgagaagaagctgcgggaagg08/12/0211/22/03113Genomicunknown
ss13717225BCM_SSAHASNP|chr3.NT_005612.14_32143363fwd/BC/Tcactgggaggcgctgctcaaaagggtttgcctgagactccgagaagaagctgcgggaagg11/05/0311/22/03120Genomicunknown
ss22024547SSAHASNP|WGSA-200403-chr3.chr3.NT_005612.14_32143363fwd/BC/Tcactgggaggcgctgctcaaaagggtttgcctgagactccgagaagaagctgcgggaagg03/20/0403/20/04126Genomicunknown
ss22987929BCM_SSAHASNP|BCM_HTWB_SNPS_200403.chr3.NT_005612.14_32143363fwd/BC/Tcactgggaggcgctgctcaaaagggtttgcctgagactccgagaagaagctgcgggaagg03/22/0403/22/04126Genomicunknown
ss23359323PERLEGEN|afd4344381byFreqfwd/BC/Tcactgggaggcgctgctcaaaagggtttgcctgagactccgagaagaagctgcgggaagg08/10/0409/13/04126Genomicunknown
ss42077750ABI|hCV32860786byFreqfwd/BC/Tcactgggaggcgctgctcaaaagggtttgcctgagactccgagaagaagctgcgggaagg07/17/0511/03/06126Genomicunknown
ss96049494HUMANGENOME_JCVI|1103656219955fwd/BC/Tcactgggaggcgctgctcaaaagggtttgcctgagactccgagaagaagctgcgggaagg03/25/0803/25/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3187686|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GTGCTTTTTT CAAGACAGGA ATCAAAATGT TAGGAACACG GCAGAAAGGT GACACCTGGA
 GACCAAACGC AGGATAAGGA GTACTGCAGA GGTCACAGGG AAGTCACAGA ACAGTAATAC
 GCTAGCAGGG GCATGGGGCA TGAAGAACAG AAGAAGAGAG GAAGTGTTTC CGAGCCTCCG
 GAAAAGAAAT CAGAGCCAAG CACAGCTTCC CGGGTCACAG AACCAATTCA TTCACCAGGC
 GGCACCACTG CCGTCATTTC AGCTTCTGGC CACTGGGAGG CGCTGCTCAA AAGGGTTTGC
 Y
 CTGAGACTCC GAGAAGAAGC TGCGGGAAGG ACAGCAGGGG TCCCGGGGTT TTAGCCTCTG
 GCCCAGGAGT TGTATGTCCA TAACCAAAGG GAGCACAGTC TGCACCCAGC TCTCATCCCA
 TCGGAGCTGC TGCGACTCCC GCAGGTTCTT CCAAAACTGG TTTAGCTTGC CTGCAGGATC
 AGGAAAGTTT GAGAAAAGCA TCTGCAAAAA AATAAAGAGC AGAGCTTACC TCATTGCCTG
 TCCCCACCCC ATCCCAGGTC ACCACCTGGC TGACCCCAGG TCCCCGACCC AACAACAACC

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_022411.6 ABBA01016401 Hs.44592
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 HWP C
 T
ss23359323 AFD_EUR_PANEL European 46 IG 0.739 0.261 0.479 0.870 0.130
AFD_AFR_PANEL African American 38 IG 0.474 0.526 0.150 0.737 0.263
AFD_CHN_PANEL Asian 48 IG 0.958 0.042 1.000 0.979 0.021
ss42077750 HapMap-CEU European 116 IG 0.793 0.207 0.403 0.897 0.103
HapMap-HCB Asian 86 IG 0.884 0.116 0.752 0.942 0.058
HapMap-JPT Asian 90 IG 0.711 0.289 0.856 0.144
ss4998085 JBIC-allele 1504 AF 0.885 0.115

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.197+/-0.244 406 341 15 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreq UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .