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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs716856          
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:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
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 ss44717504 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs716856 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
ss56259TSC-CSHL|TSC0009879fwd/BC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg09/06/0010/10/0386Genomic95 %
ss4199958SC_JCM|AL136089.15_13565rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc10/15/0110/10/03101Genomicunknown
ss10334844BCM_SSAHASNP|chr6.NT_007592.13_30679877rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc06/29/0310/10/03116Genomicunknown
ss12839371SC_SNP|NT_007592.13_30679877rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc10/21/0311/17/03119Genomicunknown
ss22489405SSAHASNP|WGSA-200403-chr6.chr6.NT_007592.13_30679877rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc03/21/0403/21/04121Genomicunknown
ss44717504ABI|hCV1347371byFreqrev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc07/19/0511/03/06126Genomicunknown
ss65842069KRIBB_YJKIM|KHS17863byFreqfwd/BC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg10/17/0612/16/06127Genomicunknown
ss66593493ILLUMINA|HumanHap300v1.1_rs716856fwd/TC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg11/09/0611/09/06127Genomicunknown
ss67550340ILLUMINA|HumanHap550v1.1_rs716856fwd/BC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg11/14/0611/14/06127Genomicunknown
ss67924848ILLUMINA|HumanHap650Yv1.0_rs716856fwd/BC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg11/14/0611/15/06127Genomicunknown
ss70913207ILLUMINA|HumanHap550v3.0__rs716856rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc04/20/0703/31/08130Genomicunknown
ss71511308ILLUMINA|HumanHap650Yv3.0_rs716856fwd/BC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg04/23/0704/23/07127Genomicunknown
ss74889750ILLUMINA|ILMN_Human_1M_rs716856fwd/BC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg08/28/0708/29/07129Genomicunknown
ss77829911HGSV|Cor12156_SNV_20070510.chr6_39990728rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc10/09/0710/14/07129Genomicunknown
ss78824531HGSV|Cor12878_SNV_20070510.chr6_39990728rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc10/17/0710/20/07129Genomicunknown
ss79248375ILLUMINA|HumanHap300v2.0_rs716856fwd/BC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg04/18/0711/18/07130Genomicunknown
ss83529434KRIBB_YJKIM|KHS482988fwd/BC/Tgaggatgcatgcatgctggccttgaggaacggagggtttcaatcaatggcacatactctg12/04/0712/05/07130Genomicunknown
ss85284649HGSV|Cor19240_SNV_20070510.chr6_39990728rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc11/30/0712/08/07130Genomicunknown
ss93446959BCMHGSC_JDW|JWB-2129030rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc02/26/0803/04/08129Genomicunknown
ss105995132BGI|BGI_rs716856rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc09/12/0806/18/09130Genomicunknown
ss1099935201000GENOMES|CEU.trio.12.15.2008_1503562_chr6_39990728rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc12/15/0812/17/08130Genomicunknown
ss116431244ILLUMINA-UK|NA18507_000063651_NCBI36.1_chr6_39990728rev/TA/Gcagagtatgtgccattgattgaaaccctccgttcctcaaggccagcatgcatgcatcctc01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs716856|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTCCTTTTCT TAAACGGGGT GTGATGCCTT GCTTAATACC CTCCATGTGC TGAGGAAGCA
 CTCATGGTGT CTCTTTCCTC TATGGAGGCC TGCTCCAGGT GCTGTGGAGG GGACAGAAGA
 CACATAAGAC ATTGCCCTGT CCTTACAGGC TGCTAAGGGC CAAAAGATGT CATTCCATGG
 GACAGCCTTT GCTTGTCTTG TGGTACTGAT TAAAGAGTTA CAGAGAGGAA GAAAGAACTC
 TTAGCAGGAG AGAACTAGGA GGGCTTCAAG GAGGATGCAT GCATGCTGGC CTTGAGGAAC
 Y
 GGAGGGTTTC AATCAATGGC ACATACTCTG AGGGGGAGCA GGAGTACAGA ACCTGCAAGG
 GCTCTACGGT GGGAAAGTGG GAGGTGGATC TGTGGGCTGT ACTGCCCGCA AACACGTTCT
 CCCTTTTTGT CTCTTATTTC CTGGCACATG GATTGGAGAC ATCAGATCTT CCCTCCCATT
 CATACTCTTT TGTCCACCAC CTGCCTTTGG AGGGGAGTGT TTTACAGAAA AGAAAACTTA
 TAGTTCTAGG TTATCCTAGC AGCATTATTT TTTTCAAAGC TATACATTTT TCCCTTTACC

  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 AL135840 AL136089.9 AL591053 AL592158
dbSNP Blast Analysis

  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
ss44717504 HapMap-CEU European 120 IG 0.433 0.483 0.083 0.439 0.675 0.325
HapMap-HCB Asian 90 IG 0.778 0.178 0.044 0.150 0.867 0.133
HapMap-JPT Asian 88 IG 0.750 0.227 0.023 1.000 0.864 0.136
HapMap-YRI Sub-Saharan African 120 IG 0.700 0.283 0.017 0.655 0.842 0.158
AoD_African_American 90 AF 0.710 0.290
AoD_Caucasian 92 AF 0.720 0.280
AoD_Chinese 90 AF 0.920 0.080
AoD_Japanese 90 AF 0.760 0.240
ss65842069 KHP1 180 AF 0.656 0.289 0.056 0.371 0.800 0.200

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.317+/-0.241 1207 1002 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
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .