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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs10400027          
refSNP ID: rs10400027
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_020549.3:c.1112-1157C>T
NM_020984.2:c.758-1157C>T
NM_020985.2:c.758-1157C>T
NM_020986.2:c.758-1157C>T
NT_017696.14:g.1657858C>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 ss14687916 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10400027 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
ss14687916BCM_SSAHASNP|chr10.NT_017696.14_1657858fwd/BC/Tagcccccaaggtcaggctctcctggtgatagcagccctcaccattgggtcttgaagtgac11/10/0311/22/03119Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10400027|allelePos=481|totalLen=681|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=119
 GGTCTTAAAG ATTTACTAAC CACCCTGGGA AGGGGAGCTG TCCACATGCC CAAGGAAGGC
 AAAACGCAGG CGAgagctcc caccattata tctgtgatcc aggcagcagg atggaggaag
 gtgggaagca ggacaaagag cacatgctag ttatctttga ggaggttccc cggaagctgt
 ggtgtagttt tttgagatct tgctcataga atttagacac ctggttaccc ctagctgtaa
 gggaggctgg gaagtatagc tctagtttgt tatccatgta ccaagctaaa aaccaggggt
 tctacaagca aggaaagaaa ggacatgtgg tgtgcaacta ggagtctcta ccaTGTAATG
 AACCTTTCCC TGCAAATGCC ATGCACCCAT CTTCCCACAC ACAGAGCACT CTCACCCCTG
 CCCTGGGTGC CTCATCCTGT CCCAGCATCC AGCCCCCAAG GTCAGGCTCT CCTGGTGATA
 Y
 GCAGCCCTCA CCATTGGGTC TTGAAGTGAC TCCTTGGAAT TTTAAACCAA AATGTTAAAC
 TTTGGGTGGA CTTTTTAACT TTTGGTGAAC TTTAAACCAA GAGGCAGGCT GTGTACCCCC
 ACACCCAGTA CTGAGCAGTG GAGAGAACAT CGTCAGCACA ATAGACTCCT GTTTGGAAGA
 AATGGGAACA CGCAGCGGGA

  GeneView back to top
GeneView via analysis of contig annotation: CHAT choline acetyltransferase
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_017696->NM_020549
svfunction
referenceNT_017696->NM_020984
svfunction
referenceNT_017696->NM_020985
svfunction
referenceNT_017696->NM_020986
svfunction
HuRefNW_001837975->NM_020549
svfunction
HuRefNW_001837975->NM_020984
svfunction
HuRefNW_001837975->NM_020985
svfunction
HuRefNW_001837975->NM_020986
svfunction
CeleraNW_924685->NM_020549
svfunction
CeleraNW_924685->NM_020984
svfunction
CeleraNW_924685->NM_020985
svfunction
CeleraNW_924685->NM_020986
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_017696->NM_020549->NP_0655741657858forwardintron
referenceNT_017696->NM_020984->NP_0662641657858forwardintron
referenceNT_017696->NM_020985->NP_0662651657858forwardintron
referenceNT_017696->NM_020986->NP_0662661657858forwardintron
HuRefNW_001837975->NM_020549->NP_065574219272reverseintron
HuRefNW_001837975->NM_020984->NP_066264219272reverseintron
HuRefNW_001837975->NM_020985->NP_066265219272reverseintron
HuRefNW_001837975->NM_020986->NP_066266219272reverseintron
CeleraNW_924685->NM_020549->NP_0655741481632forwardintron
CeleraNW_924685->NM_020984->NP_0662641481632forwardintron
CeleraNW_924685->NM_020985->NP_0662651481632forwardintron
CeleraNW_924685->NM_020986->NP_0662661481632forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs10400027 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_924685.1148163244439478plusCalt_assembly_1CeleraCeleraview480
10NW_001837975.221927245118291minusGalt_assembly_8HuRefHuRefview480
10NT_017696.14165785850523400plusCref_assemblyreferencereferenceview480

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_017696
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
HWPC
ss14687916HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 118IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
27021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
with2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .