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Reference SNP(refSNP) Cluster Report: rs3733890          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_001713.2:c.716G>A
NP_001704.2:p.Arg239Gln
NT_006713.14:g.29016317G>A
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 ss76894357 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3733890 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
ss4919886YUSUKE|IMS-JST087605byFreqfwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt07/24/0210/10/03107Genomicunknown
ss6479958WI_SSAHASNP|NT_006713.11_7789960fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt02/12/0310/10/03111Genomicunknown
ss10251468BCM_SSAHASNP|chr5.NT_006713.13_7814091byFreqfwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt06/27/0304/07/04116Genomicunknown
ss14845362SC_SNP|NT_006713.13_7814091fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt11/12/0311/22/03119Genomicunknown
ss23976493PERLEGEN|afd3172969byFreqfwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt08/10/0409/13/04123Genomicunknown
ss44598566ABI|hCV11646606fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt07/19/0507/19/05126Genomicunknown
ss66714172ILLUMINA|HumanHap300v1.1_rs3733890fwd/BA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt11/09/0611/09/06127Genomicunknown
ss67297670ILLUMINA|HumanHap550v1.1_rs3733890fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt11/14/0611/14/06127Genomicunknown
ss67702206ILLUMINA|HumanHap650Yv1.0_rs3733890fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt11/14/0611/14/06127Genomicunknown
ss68939814PERLEGEN|PGP03172969byFreqfwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt01/30/0703/31/08127Genomicunknown
ss70776296ILLUMINA|HumanHap550v3.0__rs3733890fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt04/20/0703/30/08130Genomicunknown
ss71352371ILLUMINA|HumanHap650Yv3.0_rs3733890fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt04/23/0704/23/07127Genomicunknown
ss74807423AFFY|SNP_M-178122fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt08/09/0708/09/07128Genomicunknown
ss75632792ILLUMINA|ILMN_Human_1M_rs3733890fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt08/28/0708/29/07129Genomicunknown
ss76894357SI_EXO|NT_006713.14_29016317fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt09/20/0709/20/07129Genomicunknown
ss79163322ILLUMINA|HumanHap300v2.0_rs3733890fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt04/18/0711/18/07130Genomicunknown
ss84153241PHARMGKB_PPII|PS206422_PA151168948_15227fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt12/06/0712/10/07130Genomicunknown
ss84159298KRIBB_YJKIM|KHS647611fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt12/04/0712/06/07130Genomicunknown
ss86237652CORNELL|hCV11646606fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt01/21/0801/21/08129Genomicunknown
ss98737204HUMANGENOME_JCVI|1103654141901fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt04/01/0804/01/08130Genomicunknown
ss1091548131000GENOMES|CEU.trio.12.15.2008_1294336_chr5_78457715fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt12/15/0812/16/08130Genomicunknown
ss1120632321000GENOMES|NA19240_2008_12_16_1160065_chr5_78457715fwd/TA/Gagctcatgaaggagggcttggaggctgcccactgaaagctcacctgatgagccagccctt12/16/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3733890|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 AGCCTGGGCA ACATGGCGAA ACCCCATATC TATAAAAAAA CAAACAAACA AACAAAAATT
 AGCCAGACGT GGTGGCACAC ACTTGTAGTC ACAGCAACTT GGGAGGCTGA GGTGGGAGGA
 TTGCTTGATC ACTTGAGGTG GAGACTGCAG TGAGCTGAGA TCACGCTACT GCACTCCAGC
 CTGGGCAACA GAGTGAGATT GTGTCTCAAA AAATGAAAAA AGAACTTCCT GATTCCTGAT
 GAAGAGAGGA GAGCTGGCCC TGCTGGTTTC TGGTGCATCC CTAAGTCTAT CATGTTCTTC
 CCACTCACAG GAGCATCCAT CATTGGTGTG AACTGCCACT TTGACCCCAC CATTAGTTTA
 AAAACAGTGA AGCTCATGAA GGAGGGCTTG GAGGCTGCCC
 R
 ACTGAAAGCT CACCTGATGA GCCAGCCCTT GGCTTACCAC ACTCCTGACT GCAACAAGCA
 GGGATTCATC GATCTCCCAG AATTCCCATT TGGTAAGACC AACATTTGAT GAATCATCTC
 AATATCTTCA TTTGATATGC ATATAAACTC AAGTAAATCT ATACCCAGAG ATCTTTTGTC
 ATAGTGAAGA GATGGCTTGG TGTCTCCTCA TGTCTTGTCC CTGGTTTCTG TCCCTGCAGC
 CAAAAGCCCC TTCGTATTAG AGAAGAGCAG AAGGAAAGGA TGGTCCCAGC TAGCAAAAAA
 GATCTCTGAA TTTAAATATA AAATCTAAGG TGAATCAGCA TCTAAACAGA CAACTAGTGA
 GTCATACTTT GGGGTTGGTG AGGATGCCCT TCATGGGAGA

  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_006763.1 ABBA01062003
dbSNP Blast Analysis
UniGene Cluster ID
80756

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
 N
ss10251468 HapMap-CEU European 120 IG 0.100 0.367 0.533 0.479 0.283 0.717
HapMap-HCB Asian 90 IG 0.067 0.444 0.489 0.584 0.289 0.711
HapMap-JPT Asian 88 IG 0.091 0.318 0.591 0.317 0.250 0.750
HapMap-YRI Sub-Saharan African 120 IG 0.033 0.450 0.517 0.200 0.258 0.742
CHMJ Asian 74 IG 0.284 0.676 0.041
ss23976493 AFD_EUR_PANEL European 42 IG 0.048 0.429 0.524 0.655 0.262 0.738
AFD_AFR_PANEL African American 44 IG 0.136 0.864 0.752 0.068 0.932
AFD_CHN_PANEL Asian 42 IG 0.143 0.429 0.429 1.000 0.357 0.643
ss4919886 JBIC-allele 1502 AF 0.231 0.769
ss68939814 HapMap-CEU European 120 GF 0.100 0.367 0.533 0.283 0.717
HapMap-HCB Asian 90 GF 0.067 0.444 0.489 0.289 0.711
HapMap-JPT Asian 90 GF 0.089 0.311 0.600 0.244 0.756
HapMap-YRI Sub-Saharan African 120 GF 0.033 0.450 0.517 0.258 0.742
ss84153241 PA151168949 480 AF 0.290 0.710
Concordant Genotype Total Sample A/A A/G G/G
ss23976493 70 4 21 38
ss68939814 269 21 106 142
ss76894357 1206 87 478 619
ss98737204 1 1
RefSNP Genotype Summary Total Individual A/A A/G G/G
rs3733890 1264 91 502 665
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
348 ss23976493 G/G PERLEGEN AFD_EUR_PANEL NA10860 71_IND_CHR_5
348 ss68939814 A/G CSHL-HAPMAP HapMap-CEU NA10860 CEPH1362.01 chr5-HapMap-CEU
348 ss76894357 N/N CSHL-HAPMAP HapMap-CEU NA10860 CEPH1362.01 r27_ch5_CEU_illumina:human_1m_beadchip
Genotype data submitted for1279 samples from1264 individualsIndividual with multiple genotypes submission:276

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .