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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs10262728          
refSNP ID: rs10262728
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_022087.2:c.-38-20154G>A
NT_007914.14:g.12347137G>A
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 ss14132542 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10262728 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
ss14132542WUGSC_SSAHASNP|chr7.NT_007914.13_12347137byFreqfwd/TA/Gtgagatgttttagtttctggtttattctggtattaatccccttttggatgaatagtttgc11/05/0310/25/06119Genomicunknown
ss22561184SSAHASNP|WGSA-200403-chr7.chr7.NT_007914.13_12347137fwd/TA/Gtgagatgttttagtttctggtttattctggtattaatccccttttggatgaatagtttgc03/21/0403/21/04126Genomicunknown
ss23126298WUGSC_SSAHASNP|WUGSC_WUchr7_SNPS_200403.chr7.NT_007914.13_12347137fwd/TA/Gtgagatgttttagtttctggtttattctggtattaatccccttttggatgaatagtttgc03/22/0403/22/04126Genomicunknown
ss42917306ABI|hCV26164607fwd/TA/Gtgagatgttttagtttctggtttattctggtattaatccccttttggatgaatagtttgc07/18/0507/18/05126Genomicunknown
ss74869166ILLUMINA|ILMN_Human_1M_rs10262728fwd/TA/Gtgagatgttttagtttctggtttattctggtattaatccccttttggatgaatagtttgc08/28/0708/29/07129Genomicunknown
ss81271123HGSV|Cor18507_SNV_20070510.chr7_151208769fwd/TA/Gtgagatgttttagtttctggtttattctggtattaatccccttttggatgaatagtttgc11/26/0711/28/07130Genomicunknown
ss1146651881000GENOMES|NA19240_2008_12_16_1700796_chr7_151402054fwd/TA/Gtgagatgttttagtttctggtttattctggtattaatccccttttggatgaatagtttgc12/18/0812/18/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10262728|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TGtttatctg ttggacaccc agattcattc cgtatcttgg ctattgtgaa taatgctgca
 gttaacatgg ggatgtagat gtctcttcga tataccaatt tcctttcctt tggataaatg
 cccagtagtg ggattgctgg ttcatatggt atgctatttg tagattttga ggagcctcta
 tactgttttc catagtggct gtactagttg atattctcac ccgcagagtg taagagttca
 tttttctctg catcctcccc agcatttgtt ggttttgttt tatttgtctt tttggtaata
 gccactctaa ctgggatgag atgatacctc attgtgcttc tgatttgctg ttccttgatg
 atttgtgata agtgaacatt ttgtcatata tttcttggcc atttgtcttc ttttgagaga
 tggctattca gatcatttgc ccatttttaa atctgatttt tttttcctgc tgagatgttt
 tagtttctgg tttattctgg
 R
 tattaatccc cttttggatg aatagtttgc ttatattttc tcccattcta taggttgtct
 tttcactctg ctgattgttt cctttgctgt atagaagttt tttagtgtga cataatccca
 tgtgtttgtt tttgcttttg ttgcctgggc ttttgaagtt gtattcataa aatattttcc
 cagattaacg tcctgaggca tttcccctgt tttctttcag tagttttata gtttcaggtc
 ttacatttag gtctttaatc cattttgagt tgattttcac atagaggtgg gaggctagtt
 tcattcctct gcatatgaat atccagtttt cccagtatca tctattgaag atactgtcct
 ttccccagtg agtattcttg gcatctttgt caataatcag ttggctgtag atattgtgga
 ttgatttctg ggttctctat tctgttccat tgctctgtat atcagttttt atgccagtac
 catgttgttt ccatcactaC

  GeneView back to top
GeneView via analysis of contig annotation: GALNT11 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_007914->NM_022087
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_007914->NM_022087->NP_07137012347137forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs10262728 maps exactly once on NCBI human chromosome 7
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
7NW_001839088.2729288145582565minusTalt_assembly_8HuRefHuRefview500
7NW_923751.11786169146328680plusGalt_assembly_1CeleraCeleraview500
7NT_079596.251133860151098292plusGalt_assembly_2CRA_TCAGchr7v2CRA_TCAGchr7v2view500
7NT_007914.1412347137151402054plusGref_assemblyreferencereferenceview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007914
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss14132542HapMap-CEUEuropean 118IG 0.051 0.949 1.000 0.025 0.975
HapMap-HCBAsian 88IG 0.045 0.114 0.841 0.020 0.102 0.898
HapMap-JPTAsian 90IG 0.089 0.267 0.644 0.150 0.222 0.778
HapMap-YRISub-Saharan African 118IG 0.339 0.542 0.119 0.294 0.610 0.390

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.376+/-0.21627021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .