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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs11666105          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/130
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
NM_014475.3:c.740T>C
NP_055290.1:p.Val247Ala
NT_011109.15:g.21714007T>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 ss44164564 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11666105 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
ss16787241CSHL-HAPMAP|CSHL-HuAA-200402.chr19.NT_011109.15_21714007fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg02/17/0403/04/04120Genomicunknown
ss44164564ABI|hCV3170906byFreqfwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg07/18/0511/03/06126Genomicunknown
ss48404976APPLERA_GI|hCV3170906byFreqfwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg09/28/0511/03/06126Genomicunknown
ss65725380ILLUMINA|Human1-rs11666105fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg10/10/0610/10/06127Genomicunknown
ss66827298ILLUMINA|HumanHap300v1.1_rs11666105fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg11/09/0611/09/06127Genomicunknown
ss66942781ILLUMINA|HumanHap550v1.1_rs11666105fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg11/14/0611/14/06127Genomicunknown
ss67104279ILLUMINA|HumanHap650Yv1.0_rs11666105fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg11/14/0611/14/06127Genomicunknown
ss70396844ILLUMINA|HumanHap300v2.0_rs11666105fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg04/18/0711/18/07127Genomicunknown
ss70535524ILLUMINA|HumanHap550v3.0__rs11666105fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg04/20/0703/30/08130Genomicunknown
ss71066823ILLUMINA|HumanHap650Yv3.0_rs11666105fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg04/23/0704/23/07127Genomicunknown
ss74806252AFFY|SNP_M-175344fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg08/09/0708/09/07128Genomicunknown
ss75872056ILLUMINA|ILMN_Human_1M_rs11666105fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg08/28/0708/29/07129Genomicunknown
ss85117232KRIBB_YJKIM|KHS903567fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg12/04/0712/08/07130Genomicunknown
ss117725855ILLUMINA-UK|NA18507_000055302_NCBI36.1_chr19_54137629fwd/BC/Tcggcctccgtgagcggcaccaagggcatggacaggtgaggcatggcgggcccaagcgctg01/19/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11666105|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TCCCAAAGTG CTGGGATTAC AGGCGTGAGC CACCGCGACC AGCCAGCACT TCATTCTTTT
 GCCTTGCCAT GCAAGAAGTG AAGTCTCTTG CCCAAGGTTC CACAGGCAGG ATTTGGGGCC
 TGTGCAGTCT CAGAGACTCT GCCCTGAGAG ACCCTGCCCT GACCCAGGAC TTCCCTCCAG
 GTGTGGATGA CACTGTCACG GTGCTCCTGC AGTACCCAGG GGAGGTCCAT GGCAGCTTCA
 CCTGCAGCAT CACCGTGCAG CTCTCCAACA CGGCCTCCGT GAGCGGCACC AAGGGCATGG
 Y
 ACAGGTGAGG CATGGCGGGC CCAAGCGCTG GGGATCGTGC CCCTAAAATA GGAGGGGGAC
 AAATGGCCTC TGGAGCTAGA TGAGAGCTTA ACCAGCCAAT TTCACATCAT TGCTAAAGAG
 TTCCTCCTTA ACCAAGCCAA GAGGTGGGTT CTGGGCCTCT AGGCTCTCCT TACTTAGGAT
 GAACCTATTG CTCTGTCAAA TATTCTTGGG CCTGGCTGGC ACGGTGGCTC ACGTCTGTAA
 TCCCAGCACT TTGGGAGGCC AAGGCAGGCA GATCACCTGA GGTCAGGAGT TCCAGACCAG

  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_011109
dbSNP Blast Analysis
UniGene Cluster ID
405755

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss44164564 HapMap-CEU European 116 IG 0.052 0.224 0.724 0.150 0.164 0.836
HapMap-HCB Asian 90 IG 0.333 0.511 0.156 0.752 0.589 0.411
HapMap-JPT Asian 88 IG 0.295 0.523 0.182 0.752 0.557 0.443
HapMap-YRI Sub-Saharan African 118 IG 0.390 0.559 0.051 0.669 0.331
ss48404976 AGI_ASP population multiple 74 IG 0.216 0.270 0.514 0.020 0.351 0.649

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.498+/-0.035 1244 1039 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
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .