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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1561403          
refSNP ID: rs1561403
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/129
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
NM_005909.3:c.287-15302T>C
NT_006713.14:g.22058626T>C
Links

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 ss2405076 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1561403 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
ss2405076TSC-CSHL|TSC0450881byFreqfwd/TA/Gtgatccatatgtatgctaatcaaagttcttgaatgtattactctttgctctttcgtaaat10/20/0005/16/0488Genomic95 %
ss4354304SC_JCM|AC093218.2_100812rev/BC/Tatttacgaaagagcaaagagtaatacattcaagaactttgattagcatacatatggatca02/19/0210/10/03103Genomicunknown
ss17047975CSHL-HAPMAP|CSHL-HuAA-200402.chr5.NT_006713.13_856400rev/BC/Tatttacgaaagagcaaagagtaatacattcaagaactttgattagcatacatatggatca02/17/0403/04/04120Genomicunknown
ss44648466ABI|hCV2109725rev/BC/Tatttacgaaagagcaaagagtaatacattcaagaactttgattagcatacatatggatca07/19/0507/19/05126Genomicunknown
ss76487022AFFY|AFFY_6_1M_SNP_A-8348036rev/BC/Taaagagtaatacattcaagaactttgattagc08/28/0708/30/07129Genomicunknown
ss93132660BCMHGSC_JDW|JWB-1991777rev/BC/Tatttacgaaagagcaaagagtaatacattcaagaactttgattagcatacatatggatca02/26/0803/03/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1561403|allelePos=996|totalLen=1188|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 CAAAGTGTGA TTTGCTTACT TTGTCTTTAG AAGTAAGCAA ATCAGGTGAT CTACCTTCAG
 GATCTGAAAA ATATACACCT GGGCCATCAT TACAAGAAAC CCACTGCCAT GCATAAATAA
 TTAAAAAGAA GACATTGCCT AGCTCTTTTC AAGTGATTAG GGCCAAAAAC TGCCCCAAAG
 TGTCAGGAGT TGTTTGTGTG TTTGGTTTTC TCACACGCGC ATTGGATTTT GCCTGTGGTC
 ATTCTGCCAC CCCTTAAGAT CTCTTAAGGA ATTAAAATGA GGCATCGTTA GATTTCATTT
 TGATTTTATA TTCAACGACA AGGTCTTCAC AAGGTCACTA TTAATGGGGT GCCACAGTAT
 GCCCCCAAAC CATATTTTTT GCTGAAGGTT GATTTCTTAC CTTAACAACG TATTTTTTAT
 TTGTTTTAAG ATGAGTACCG TTGACCTCTG GGATATTATA ATTGAAAGAA TACATCTGCT
 TATTTAGGAA AATGTGATGT AGTAAACCAA AGGAATTAAG TTCTGGGCCA TATATTTAAT
 TAATGGTTTA CTTAACAAAC AGAGATTTGT TTCTGAGGCA ATTCAACCAA ATCTGGCCAA
 TGGGCATTTT CAAGGCATTG ATAAATGTAC TCTGAACCAA CAGACGTAGC TCTCCTGAGA
 AACAGGTCTG AAACCCATGA CAAAGAGCAA GTCAAACAAG GTAGTCAAAT AAATTCTGTC
 CTCTTCTATC TTCTTTTTAA AAGACTGAAA TTTTAGTTTA AAATGAGTCC AAGGAGGGAG
 GGAAATAATC TGGGGATTTT GGGGAAAATT GCCCTTGAGC AAATCCCCAG ATTTTAATTT
 CCATGAGAAG TAACAAGTTC TCTTAAGAAA GGCAGCATGC ATAAAATCAC TTTCTACATT
 CCTGTCTTGC ATTATTCTCC ATTGGGTATT TTTTATGTAT TTATATACAC TTGGAATATA
 TGCAATGATC CATATGTATG CTAATCAAAG TTCTT
 R
 GAATGTATTA CTCTTTGCTC TTTCGTAAAT AAAATAGTAT AAATTGGGAG CATATTTTGT
 CTCTGTAAAA ATGCCAACAG GTAAGCCGGC CCTAGAGAAA AATGGACCAA ATCAAGCTCT
 GCCAGAGCTC TGGAGTTTAA CTGAAAGAAA GAACATCTGA TTCCTGCCCA GAAAGCAACA
 CTGAACACCT CA

  GeneView back to top
GeneView via analysis of contig annotation: MAP1B microtubule-associated protein 1B
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_006713->NM_005909
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_006713->NM_005909->NP_00590022058626forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1561403 maps exactly once on NCBI human chromosome 5
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
5NW_001838951.175157966669688minusTalt_assembly_8HuRefHuRefview995
5NW_922729.175954367359699minusTalt_assembly_1CeleraCeleraview995
5NT_006713.142205862671500024minusTref_assemblyreferencereferenceview995

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_006713 AC012609
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss2405076CEPH 184AF 0.680 0.320
HapMap-CEUEuropean 120IG 0.217 0.467 0.317 0.450 0.550
HapMap-HCBAsian 90IG 0.311 0.689 0.156 0.844
HapMap-JPTAsian 90IG 0.111 0.289 0.600 0.256 0.744
HapMap-YRISub-Saharan African 120IG 0.250 0.533 0.217 0.517 0.483

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.463+/-0.13127021000

  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 .