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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs3901          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:36/130
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
NT_011875.11:g.7873808T>C
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 ss3938 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3901 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
ss3938OEFNER|M10byFreqfwd/BC/Tgaatttttttgtttattcccaatgatcttaagcacttgtaaagtttttacattagttaca01/23/9904/07/0436Genomicunknown
ss69277834PERLEGEN|PGP13177670fwd/BC/Tgaatttttttgtttattcccaatgatcttaagcacttgtaaagtttttacattagttaca01/30/0701/30/07127Genomicunknown
ss75003336ILLUMINA|ILMN_Human_1M_rs3901fwd/BC/Tgaatttttttgtttattcccaatgatcttaagcacttgtaaagtttttacattagttaca08/28/0708/29/07129Genomicunknown
ss76429458AFFY|AFFY_6_1M_SNP_A-8290282fwd/BC/Tattcccaatgatcttaagcacttgtaaagttt08/28/0708/30/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3901|allelePos=156|totalLen=343|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 gcattgctat aagttacctg caatttataa agttgtgaaa tagttcaaga caatgaAGGG
 AGAGACTCTC TGGTAACTAC AGAGTATGAG CTCATCATTG CTTAGTTTCC ACAAGAGGTA
 TCTCTGAATT TTTTTGTTTA TTCCCAATGA TCTTA
 Y
 AGCACTTGTA AAGTTTTTAC ATTAGTTACA AAATGCAATT TGAAGTGAAA GAAACAGAAA
 TACAAAATAT TAGTTTCTCT TTTTCTCCTA CATTCCTACA TGGATTTGTA GAAGAGCTGA
 CCTTTACTTA TAAAATAAAT CAGCAAATGA GTGTCTTTTC TAGAATGGGG TGACCCAATT
 TTTATTA

  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
dbSTS GenBank
G42826 NC_000024.7
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source T/T
 HWP C
 T
ss3938 Global 718 AF 0.001 0.999
TSC_42_AA 84 AF 0.030 0.970
TSC_42_C 84 AF 1.000
TSC_42_A 84 AF 0.050 0.950
HapMap-CEU European 60 IG 1.000 1.000
HapMap-HCB Asian 44 IG 1.000 1.000
HapMap-JPT Asian 44 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 60 IG 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
525 409 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
byClusterbyFreqwithHapMapFreq YES YES YES

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Revised: May 25, 2006 1:38 PM .