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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs6022990          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:114/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NG_008334.1:g.19985T>C
NM_000782.3:c.1121T>C
NM_000782.4:c.1121T>C
NM_001128915.1:c.1121T>C
NP_000773.2:p.Met374Thr
NP_001122387.1:p.Met374Thr
NT_011362.9:g.17828440A>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 ss8325975 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6022990 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
ss8325975SC_SNP|NT_011362.7_17828390fwd/TA/Ggattctttcagacaggcttttaaatacggctattcctcaaatcttctgcccgtggcacct04/17/0310/10/03114Genomicunknown
ss48293890SNP500CANCER|CYP24A1-43byFreqrev/BC/Taggtgccacgggcagaagatttgaggaatagccrtatttaaaagcctgtctgaaagaatc08/19/0511/03/06126Genomicunknown
ss48430604APPLERA_GI|hCV25620114rev/BC/Taggtgccacgggcagaagatttgaggaatagccgtatttaaaagcctgtctgaaagaatc10/02/0511/30/05126Genomicunknown
ss84156808PHARMGKB_AB_DME|PS206220_PA149717519_301fwd/TA/Ggattctttcagacaggcttttaaatacggctattcctcaaatcttctgcccgtggcacct12/06/0712/10/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6022990|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 CAGAGGCTCA AAAGCAAAGC TTTCTCTGTG TCCTATTATA TAATAATATA GCTCTTTTGT
 GAGCCTCCAT CTCATAACCT TCAATCATGC CCCTATCTTA ATTAGTGCTT ACAGCGTTCA
 TTAGAGTAGC AAGATTATTG AATTAAAGGG GAGGGCACTG GCTTTCCAAG ATTTAATAGA
 ATTTGCCCAA ATGATTTAGG AAATGAGTGC CAGAAAAGAA ATATGGCTCC AAAGATTTTT
 TTGCAGTGTG ATAATTGTTT CTAATTAGCT AGGGGAAGCC GCCCATGAGT AGGGGACCAC
 TTGTTTTGTG TTTACGAGAA CAGTGTTCTA ACACATTTAT ATTGGCTCAG AGATAGGCTC
 TTACCTCATA GATTCTTTCA GACAGGCTTT TAAATACGGC
 R
 TATTCCTCAA ATCTTCTGCC CGTGGCACCT GATTCTCAGG TAATACACTT TGAATTTCCT
 TAAGAAGCTT TTGTTGCACT TGGGGATTAC GGGATAAATT GTAGAGAATC CACATTAGAC
 TGTTTGCTGT CTGCAAGCCA AATGGACATA AACTTGAGTT TTTGTAAATA ACTGCATTAA
 ACCACTATTA GCTGAAAAAA AGGTGATGCC CACCACCTTA TTCTGCAAAT GTATCAGTGA
 AGCTCTTTCA CGCGTCCTTA TAGCTACGCC TTTAGACAAA TCCAATATAT AAAAAAGCAG
 ACTTATTTCA TAAAACATAT CAATTAAGGA TATATTTTAA ATTATTTACT GAGGGAATCA
 AAGTATAATC CTTTAATCAG CTGCTTTAGA ACATTTAAAT

  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_011362
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 HWP A
 G
ss48293890 P1 202 AF 0.931 0.069 0.752 0.965 0.035
CAUC1 60 AF 1.000 1.000
AFR1 48 AF 0.708 0.292 0.403 0.854 0.146
HISP1 46 AF 1.000 1.000
PAC1 48 AF 1.000 1.000
ss48430604 AGI_ASP population multiple 74 IG 0.973 0.027 1.000 0.986 0.014
ss84156808 PA149717520 354 AF 0.983 0.017

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.061+/-0.163 38 38 0 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 UNKNOWN

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Revised: May 25, 2006 1:38 PM .