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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs11593762          
refSNP ID: rs11593762
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/129
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_000429.2:c.92-819C>T
NT_030059.12:g.794680G>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 ss38513397 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11593762 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
ss16476824CSHL-HAPMAP|CSHL-HuAA-200402.chr10.NT_030059.11_794680fwd/TA/Gccacacccaagtacatgactccacccataaaattctacaagataacccctatacatcatt02/17/0403/04/04120Genomicunknown
ss20637564SSAHASNP|WGSA-200403-chr10.chr10.NT_030059.11_794680fwd/TA/Gccacacccaagtacatgactccacccataaaattctacaagataacccctatacatcatt03/18/0403/18/04121Genomicunknown
ss38513397ABI|hCV438739byFreqfwd/TA/Gccacacccaagtacatgactccacccataaaattctacaagataacccctatacatcatt07/15/0511/02/06126Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11593762|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=126
 TGTTAGCCAC TGCGCCCGGT CAAAATCAGC TCTTCTAGGA GTCTAACGCA ACTCACACAT
 AAACAAACAC ACACGCATTC TTCTAAATAA AAAATCTCTC ATTCCTCATC ATGTTCCCTT
 TAATTCTAAC ATCTACAAAA GTCCTGAAAA TGAACTTAAA AATAGTTAAG AAGTCAATTT
 TACCTCTTTG CCAAGAGGTA AAATCAGACG GCTCAAACAG CTGCATTGCA TGGCAGGTTC
 CACAAGATGC AATGCACCGT ATATAAAACA CCACACCCAA GTACATGACT CCACCCATAA
 R
 AATTCTACAA GATAACCCCT ATACATCATT GTTGTTTTGC AGAATACTTC CATAAGCAGC
 TCTCAGATCT CCCACATGGT CACTCAGCCT CCCGAAAGCC AGGTGTCCTT AGAGCTGGGC
 TTGACCTCTT CAATTACTGT AGGACTGACA AGGGTTCAAC ATGAGCTGGA ATTTGATTTT
 ATTCTTCCAC TATTTGCCTT AAAGACTCTG CAGGGTCTAA AATGTAAAGC ACTAAATGGT
 GCTTGTAGGA AAATCTACTC TTGCTTTGGG GTTATGCAAA CTGTCAATAT CTACAAATTA

  GeneView back to top
GeneView via analysis of contig annotation: MAT1A methionine adenosyltransferase I, alpha
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_030059->NM_000429
function
"
Group
label
Contig-->mRNA-->ProteinContig
position
mRNA
orientation
mRNA
pos
FunctiondbSNP
allele
Protein
residue
Codon
pos
Amino acid
pos
referenceNT_030059->NM_000429->NP_000420794680reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs11593762 maps exactly once on NCBI human chromosome 10
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
10NW_001837991.2431773175889373minusTalt_assembly_8HuRefHuRefview300
10NW_924862.192627076036510plusGalt_assembly_1CeleraCeleraview300
10NT_030059.1279468082036144plusGref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_030059
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL359195.24 AL357792.16

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/G
G/G
HWPA
G
ss38513397HapMap-CEUEuropean 120IG 0.067 0.933 1.000 0.033 0.967
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 1.000 1.000
AoD_Caucasian 92AF 0.040 0.960

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.019+/-0.09527021000

  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 .