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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs3743904          
refSNP ID: rs3743904
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_004204.2:c.1594-116A>G
NM_148920.1:c.1532-116A>G
NT_037887.4:g.572768A>G
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 ss90284605 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3743904 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
ss4929911YUSUKE|IMS-JST095196byFreqfwd/TA/Gtgggaactgggactggcttctcccacaggcagggaatgtctgagacagcactggccctgc08/01/0210/10/03107Genomicunknown
ss16718980CSHL-HAPMAP|CSHL-HuAA-200402.chr16.NT_037887.3_572768byFreqfwd/TA/Gtgggaactgggactggcttctcccacaggcagggaatgtctgagacagcactggccctgc02/17/0408/05/04120Genomicunknown
ss23467576PERLEGEN|afd4603940byFreqfwd/TA/Gtgggaactgggactggcttctcccacaggcagggaatgtctgagacagcactggccctgc08/10/0409/13/04123Genomicunknown
ss79824099HGSV|Cor18507_SNV_20070510.chr16_572768fwd/TA/Gtgggaactgggactggcttctcccacaggcagggaatgtctgagacagcactggccctgc11/23/0711/23/07130Genomicunknown
ss82842981HGSV|Cor18555_SNV_20070510.chr16_572768fwd/TA/Gtgggaactgggactggcttctcccacaggcagggaatgtctgagacagcactggccctgc11/27/0712/03/07130Genomicunknown
ss90284605BCMHGSC_JDW|JWB-0906706fwd/TA/Gtgggaactgggactggcttctcccacaggcagggaatgtctgagacagcactggccctgc02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3743904|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GGCCCATTCT GCCCTGTGTC GGAGGCGCCC TTGGCTGGCT GGGGCTGCCC TGGGCCCCAC
 AGGGCTCAAG TTCTGGGTGG AACAGAACCG ACTGAGTGAG TCCTGGGGTG GGGTGTGCGT
 CCCTGTGGCA CGGCCCCTCA GAGTTGGGCA GCCCCGAGGG GAGATGCAGC TTCTGCCTCC
 CCCCAGCGCT CCCTTCTGGC TGCAGGCTCA CTTGCCTCCT TGGGAACTGG GACTGGCTTC
 TCCCACAGGC
 R
 AGGGAATGTC TGAGACAGCA CTGGCCCTGC CTCACAACTG CCCGCCCCCA CCCTCTCTCT
 GCAGACGGGG TTGGAGCTCA GACCACCCCA CTGACCGCTG CCCTTGTCCT TCCAGATAAA
 CCCACTGCCC TACAGCCGCG TGGTGCACAC CTACCGCCTC CCCAGCTGTG GCTGCCACCC
 CAAGCACTCC TGGGGCGCCC TGTGCCGCAA GCTGTTCCTT GGGGAGCTCA TCTACCCCTG
 GAGGCAGAGA

  GeneView back to top
GeneView via analysis of contig annotation: PIGQ phosphatidylinositol glycan anchor biosynthesis, class Q
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_037887->NM_004204
function
referenceNT_037887->NM_148920
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_037887->NM_004204->NP_004195572768forwardintron
referenceNT_037887->NM_148920->NP_683721572768forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs3743904 maps exactly once on NCBI human chromosome 16
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
16NW_001838339.22069291554726minusCalt_assembly_8HuRefHuRefview200
16NT_037887.4572768572768plusAref_assemblyreferencereferenceview200
16NW_926018.1549195833545plusAalt_assembly_1CeleraCeleraview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_037887
dbSNP Blast Analysis
GenBank HTGS Finished:
Z98883.5

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss16718980HapMap-CEUEuropean 118IG 0.407 0.356 0.237 0.050 0.585 0.415
ss23467576AFD_EUR_PANELEuropean 44IG 0.409 0.318 0.273 0.100 0.568 0.432
AFD_AFR_PANELAfrican American 42IG 0.238 0.429 0.333 0.584 0.452 0.548
AFD_CHN_PANELAsian 42IG 0.048 0.571 0.381 0.200 0.333 0.667
ss4929911JBIC-allele 1474AF 0.282 0.718

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.499+/-0.01615211090

  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
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .