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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs28381223          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:125/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_001461.1:c.1518G>T
NP_001452.1:p.Arg506Ser
NT_034400.4:g.199180C>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 ss105439442 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28381223 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
ss35072938EGP_SNPS|FMO5-039651byFreqfwd/BG/Tgaagcctctgatgacaagagtagttgaaagagtagttctatgacttcaacaatgacaata03/02/0511/02/06125Genomicunknown
ss74877081ILLUMINA|ILMN_Human_1M_rs28381223fwd/BG/Tgaagcctctgatgacaagagtagttgaaagagtagttctatgacttcaacaatgacaata08/28/0708/29/07129Genomicunknown
ss86243217CORNELL|hCV25597089rev/BG/Ttattgtcattgttgaagtcatagaactactctttcaactactcttgtcatcagaggcttc01/21/0801/21/08129Genomicunknown
ss105439442SNP500CANCER|FMO5-07fwd/BG/Tgaagcctctgatgacaagagtagttgaaagagtagttctatgacttcaacaatgacaata09/05/0809/05/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs28381223|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 ATTATTGACA GGCCATGGTT TCTGTCTTTT CTACTTTAGG TATGTGGAGA GCCAACGCCA
 TACCATTCAG GGAGACTACA TAGATACCAT GGAAGAGCTT GCTGATTTGG TGGGGGTCAG
 GCCCAATCTG CTGTCTCTGG CCTTCACTGA CCYCAAGCTG GCATTACACT TATTACTGGG
 ACCCTGCACT CCAATCCACT ATCGTGTACA GGGCCCTGGA AAGTGGGATG GGGCTCGAAA
 AGCTATCCTC ACCACAGATG ATCGCATCAG GAAGCCTCTG ATGACAAGAG TAGTTGAAAG
 K
 AGTAGTTCTA TGACTTCAAC AATGACAATA GGCAAGTTTA TGCTAGCTCT TGCCTTCTTT
 GCTATAATTA TAGCTTACTT CTAGTTGTCC TATTGTCACT GCCCTGTTTT TCATTGGGAA
 GCTTATCTAC AGATGCCTTC AGAATCTGAC GAGATTGACT CTCAGTTTCA TATTGCCCAG
 AAATCTACTT TAATGTCTCT TTYGAAAGCA TTAATTCACT TTCCTTTTTC CTACAATGAA
 ACCTGTTTTC CATTTGTATT AACTCATCTC CCTTCCACTC ATGATCCGTC ACTCTTCCTT

  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
AY902236
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source G/G
 G/T
 HWP G
 T
ss105439442 P2 420 GF 0.990 0.010 0.995 0.005
CAUC2 120 GF 1.000 1.000
AFR2 120 GF 0.967 0.033 0.983 0.017
P3 554 GF 0.996 0.004 0.998 0.002
CAUC3 132 GF 1.000 1.000
AFR3 148 GF 0.986 0.014 0.993 0.007
HISP3 98 GF 1.000 1.000
PAC3 176 GF 1.000 1.000
ASI2 180 GF 1.000 1.000
ss35072938 EGP_YORUB-PANEL Sub-Saharan African 22 IG 0.818 0.182 0.752 0.909 0.091
EGP_HISP-PANEL Hispanic 42 IG 1.000 1.000
EGP_CEPH-PANEL European 40 IG 1.000 1.000
EGP_AD-PANEL African American 30 IG 1.000 1.000
EGP_ASIAN-PANEL Asian 44 IG 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.007+/-0.061 897 720 58 0

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

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Revised: May 25, 2006 1:38 PM .