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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2854482          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_001135241.1:c.137T>A
NM_001354.4:c.137T>A
NM_205845.1:c.137T>A
NP_001128713.1:p.Phe46Tyr
NP_001345.1:p.Phe46Tyr
NP_995317.1:p.Phe46Tyr
NT_077567.3:g.4983821A>T
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 ss76893403 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2854482 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
ss4041394SC_JCM|L32592.1_4986byFreqfwd/TA/Taggccgtcaaattggcaatagaagccgggtccaccatattgattctgcacatgtttacaa09/26/0110/25/06100Genomicunknown
ss69068270PERLEGEN|PGP04759088byFreqrev/A/Tttgtaaacatgtgcagaatcaatatggtggacccggcttctattgccaatttgacggcct01/30/0708/14/07127Genomicunknown
ss74858985ILLUMINA|ILMN_Human_1M_rs2854482fwd/A/Taggccgtcaaattggcaatagaagccgggtccaccatattgattctgcacatgtttacaa08/28/0708/29/07129Genomicunknown
ss76893403SI_EXO|NT_077567.3_4983821rev/A/Tttgtaaacatgtgcagaatcaatatggtggacccggcttctattgccaatttgacggcct09/20/0709/20/07129Genomicunknown
ss1152884721000GENOMES|NA19240_2008_12_16_2063558_chr10_5033821rev/A/Tttgtaaacatgtgcagaatcaatatggtggacccggcttctattgccaatttgacggcct12/18/0812/19/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2854482|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 TTCCTTGTGT TAATTTCACC ATACTAAAAA TAATTAAGAT TATGTCTGTA ACTATAGTTG
 CGTCCTGTTG ATTTTTCCAA AAAATCACTG AAAGTGAAAT TGTTTTGGGG ACACTTCCAA
 GCTAGTGGTC AAGCAGTGAT TTTTCTGGGA CTGCAGAAGT TCCTGCTATG CCCAACCTTT
 ATTACTAAAT GGGAAAGACC CAGTCAGACT GGGATGGGCT TATGATTCTA CATACAGAGC
 TCATCCAAGA AAGGAGGAAA AGCTGATTTT TGTGAACGTT GCTGCTTGTG CCCGAACTAA
 CTCTCAGGCA CATTAGTCAG AAAATATTAC GTTTGGTTGC TCCCCCAGGT TCCTAAAAGT
 AAAGCTCTAG AGGCCGTCAA ATTGGCAATA GAAGCCGGGT
 W
 CCACCATATT GATTCTGCAC ATGTTTACAA TAATGAGGAG CAGGTTGGAC TGGCCATCCG
 AAGCAAGATT GCAGATGGCA GTGTGAAGAG AGAAGACATA TTCTACACTT CAAAGGTACT
 GTGCCTATGA TGAGCTTGTG TGCACATGTA TTTATTGTGA TTGTGTGGAG GTGGCAGTTC
 TATGACTGGA TCCATAGTTG AGGGTGAATT GTGCTTATTT ATTTCGATTT ATTCACACTT
 ACTCATGTAT TAAAACTAAT ATCAAAGGCA GGAAGTGAAG ATGGCTTTCT CATCTTTGCA
 GTGTTCCAAT TCATGCCTTC AAAGTGCCTT TACTCTTCGA GCTCAGCACA GATCAATATG
 GTTTAACATA GACTATAGAA TGAGAGATAA TCTTAATCAT

  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_077567.3 AB032151
dbSNP Blast Analysis
UniGene Cluster ID
498513

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/T
 T/T
 HWP A
 T
ss4041394 HapMap-CEU European 118 IG 0.119 0.881 0.655 0.059 0.941
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.033 0.233 0.733 0.527 0.150 0.850
ss69068270 HapMap-CEU European 120 GF 0.117 0.883 0.058 0.942
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.033 0.217 0.750 0.142 0.858
Concordant Genotype Total Sample A/A A/T T/T
ss69068270 269 233 32 3
ss76893403 524 231 33 3
RefSNP Genotype Summary Total Individual A/A A/T T/T
rs2854482 525 233 33 3
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5263 ss69068270 A/A CSHL-HAPMAP HapMap-YRI NA18861 YOR024.02 chr10-HapMap-YRI
5263 ss76893403 A/T CSHL-HAPMAP HapMap-YRI NA18861 YOR024.02 r27_ch10_YRI_illumina:golden_gate_1.0.0
Genotype data submitted for525 samples from525 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .