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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1052661          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_000847.3:c.211A>C
NP_000838.3:p.Ile71Leu
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 ss105439844 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1052661 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
ss1529206LEE|507699fwd/TA/Cgatgggatgaagttggtacagaccagagccttctcaactacattgccagcaaatacaacc09/13/0010/10/0386cDNAunknown
ss14536484WUGSC_SSAHASNP|chr6.NT_007592.13_43564313rev/BG/Tggttgtatttgctggcaatgtagttgagaaggctctggtctgtaccaacttcatcccatc11/05/0311/22/03119Genomicunknown
ss70355522EGP_SNPS|GSTA3-009226byFreqfwd/TA/Cgatgggatgaagttggtacagaccagagccttctcaactacattgccagcaaatacaacc04/18/0708/14/07127Genomicunknown
ss78916606HGSV|Cor18507_SNV_20070510.chr6_52875164rev/BG/Tggttgtatttgctggcaatgtagttgagaaggctctggtctgtaccaacttcatcccatc10/19/0710/21/07129Genomicunknown
ss84168858PHARMGKB_AB_DME|PS206043_PA149840709_301rev/BG/Tggttgtatttgctggcaatgtagttgagaaggctctggtctgtaccaacttcatcccatc12/06/0712/09/07130Genomicunknown
ss105439844SNP500CANCER|GSTA3-02fwd/TA/Cgatgggatkaagttggtacagaccagagccttctcractacattgccagcaaatacaacc09/05/0809/05/08130Genomicunknown
ss116470068ILLUMINA-UK|NA18507_000078506_NCBI36.1_chr6_52875164rev/BG/Tggttgtatttgctggcaatgtagttgagaaggctctggtctgtaccaacttcatcccatc01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1052661|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 GGATGGGGAA TAAAAACATA AATGAAATAA CAGGYTAAAA GGTCAAAGGA ATCAGGTCAG
 AAAAAGAACT ACAGGCAGCT AAAATCAAAA TACTATTTCG TTTTTGAGGT TAGCAGGCAA
 TAATTTCTTT TTCATTTTAT AACCTCAGTC ATTTCAACCA TCATTTTTCT TCCTGAAATA
 STGGGATTCA TAGAAATTTC ATGTTCCTTT TTTTTCCTTC TTTCTAAAGA TGGGAGTTTG
 ATGTTCCAGC AAGTACCAAT GGTTGAGATT GATGGGATKA AGTTGGTACA GACCAGAGCC
 M
 TTCTCRACTA CATTGCCAGC AAATACAACC TCTACGGGAA AGACATAAAG GAGAGAGCCC
 TGTACGGTAT ATTTTGTGTT CTTCCATCCA CAGAGAACAC AGAGTGATTT AGGTCCTTCC
 TTGAGTGGGT RAGACCATGA CAGGGCATCA TGACCAGGAG CAGGCTGGGC CTTGGGYRTG
 TATACTGAGG TCCAGTATTG CAGAGTCCCA TGGGGATGAG GRAACAGTGA ACRTGAGGAG
 GGTTCAGGTG AGTGTGATTC TAGAAGAGGA TGCATTCCAT GGATCCAGCA CCCTGACAGA

  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_007592 Hs.102484
dbSNP Blast Analysis
UniGene Cluster ID
102484

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/C
 C/C
 HWP A
 C
ss105439844 P1 202 GF 0.941 0.059 0.970 0.030
CAUC1 62 GF 1.000 1.000
AFR1 48 GF 0.750 0.250 0.875 0.125
HISP1 46 GF 1.000 1.000
PAC1 46 GF 1.000 1.000
P2 388 GF 0.923 0.077 0.961 0.039
CAUC2 108 GF 1.000 1.000
AFR2 112 GF 0.732 0.268 0.866 0.134
P3 550 GF 0.924 0.073 0.004 0.960 0.040
CAUC3 130 GF 1.000 1.000
AFR3 148 GF 0.716 0.270 0.014 0.851 0.149
HISP3 98 GF 1.000 1.000
PAC3 174 GF 1.000 1.000
ASI2 168 GF 1.000 1.000
ss14536484 HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
ss70355522 HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
EGP_YORUB-PANEL Sub-Saharan African 24 AF 0.917 0.083 0.958 0.042
EGP_HISP-PANEL Hispanic 44 AF 0.955 0.045 0.977 0.023
EGP_CEPH-PANEL European 44 AF 1.000 1.000
EGP_AD-PANEL African American 30 AF 0.867 0.133 0.933 0.067
EGP_ASIAN-PANEL Asian 48 AF 1.000 1.000
ss84168858 PA149840710 352 AF 0.974 0.026

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.062+/-0.164 246 246 24 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 YES

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Revised: May 25, 2006 1:38 PM .