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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs9786608          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NT_011896.9:g.14423C>T
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 ss13606916 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9786608 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
ss13606916WI_SSAHASNP|chrY.NT_011896.8_14423byFreqfwd/BC/Tggtctcaatctcttcaccctgtgatccgctgccttgacctctcgaagggctgggattaca11/05/0303/31/08119Genomicunknown
ss69277861PERLEGEN|PGP13083226byFreqfwd/BC/Tggtctcaatctcttcaccctgtgatccgctgccttgacctctcgaagggctgggattaca01/30/0703/31/08127Genomicunknown
ss115580850ILLUMINA-UK|NA18507_000000002_NCBI36.1_chrY_2723943fwd/BC/Tggtctcaatctcttcaccctgtgatccgctgccttgacctctcgaagggctgggattaca01/15/0901/15/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9786608|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CAGGATTATA ATGTATTGAC GCTACTCCCA GAGTAAGGGT GGGTTATGAG TCATGGGTGT
 GGTTCCCTTA TTATTAACAT AGGGGCACCA ACTGAGTTAA GTGCCCTGCA GTTGGTGTCA
 CCCGAATTTG AAGAAAACTC TCTTTATGGC AAGACTTACG AGATTTCATA ACAAAAACCA
 TTACTTTTGA ATTTTAGAAT ATAGGGTAGG ATAGGCTAGC TATTACGCtt tttttattat
 tgtttattta tttatttatt tatttatttt ttttgagaca aagtctcgct ctgttgccag
 gctggggtgc agcggcgcaa tctcagctta ctgcaacctc tgcctcatga gttcaaatga
 ttcttctgcc tcagcctccc gagtaactgg gattacaggc acatgtcacc acgcccagct
 aattttttgt atttttagta gagacccagt ttcaccatgt tggccaggat ggtctcaatc
 tcttcaccct gtgatccgct
 Y
 gccttgacct ctcgaagggc tgggattaca ggtgtgaccc acagcaccca gccTATTATA
 CATTCTTGTG TGGCATTTAC TGAAATGAGT CTTATCAGTA GGTCAATTAA TCACATCATC
 CCCTGTCATA CCAGCTAATG TGCTGTTCTA ATGTTGAAGA GCTTTAATGA ATGCTTTTTA
 AGTGTTGCCA GTCGTTTTCC TGCATAGACG ATGCCCACCA AGGCAGACGA GAAGTGTTGA
 GAAGGGTAAC AAAATGCAAA CCCAGCAGGC CTCTTCTGTA AGTTGTCAGC ATAATGTTGA
 GCCCTCTGTA GGAAGAGGTT CATTTTTCCT TTCATAGGTC AGAGAAGAAG AACAGAAGAT
 TATGGGCCGA AATAGCAGTG TTTTGTAGGT ACTTGGCAGA GCAGTTCTTT CCCATCAAAC
 AAAATGACAG TGGAACTTTT ATCTCAGTCA TTATTAGAAT ATTGGCAGCC TGAGGATTAT
 GGGCTGGGAG TACATACCAA

  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_011896
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 T/T
 HWP C
 T
ss13606916 HapMap-CEU European 54 IG 1.000 1.000
HapMap-HCB Asian 42 IG 1.000 1.000
HapMap-JPT Asian 38 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 56 IG 1.000 1.000
ss69277861 HapMap-CEU European 12 GF 1.000 1.000
HapMap-HCB Asian 12 GF 1.000 1.000
HapMap-JPT Asian 8 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 42 GF 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.467+/-0.124 525 409 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 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .