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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs28938798          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:125/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_014440.1:c.188T>C
NP_055255.1:p.Ile63Thr
NT_022135.15:g.2472161T>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 ss37042401 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28938798 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
ss37042401PGA-UW-FHCRC|IL1F6-010794byFreqfwd/BC/Tagacccttgagaaagacagagggaaccccactacctgggcctgaatggactcaatctctg04/07/0511/02/06125Genomicunknown
ss74869096ILLUMINA|ILMN_Human_1M_rs28938798fwd/BC/Tagacccttgagaaagacagagggaaccccactacctgggcctgaatggactcaatctctg08/28/0708/29/07129Genomicunknown
ss1107517191000GENOMES|NA19240_2008_12_16_405194_chr2_113480709fwd/BC/Tagacccttgagaaagacagagggaaccccactacctgggcctgaatggactcaatctctg12/16/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs28938798|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GAAAGACTGA CTTTTCTAAT GGAAAGTGTT CCCCAAACAT AGGATGGGTG TCCCGGTTAG
 GTGGTGGGTG GTGAGGTGAC CATTCTATGA GTGCACTGTG AGTGTCAGTT AGCAGATTCC
 CTTAAAACTC TGGCTCAGAG GTACCACCCT GGAAATGGCA GCTGAACACC ACTTTTCACA
 TCGTGTTCCC AGTCACTATT GCCTTAATCT CATGCCGACA TGTGGAGACC CTTGAGAAAG
 ACAGAGGGAA CCCCA
 Y
 CTACCTGGGC CTGAATGGAC TCAATCTCTG CCTGATGTGT GCTAAAGTCG GGGACCAGCC
 CACACTGCAG CTGAAGGTGA GTGTGGAAGA CAGGTCCTGC CATTTATTTG ATGGAAACTC
 AGATTTCAGG ATCTTTTAAA AGACAATGTA CTTATTATGC TCATGCATTT TTATTTTTGG
 TTTCCTTGGG GTTGGTATAT GTTATGAAAG ACTAAGAAAA ATTGCAGGGA CATTTTGAAA
 CAAACCTACT AAAAT

  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
AY944686
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/T
 T/T
 HWP C
 T
ss37042401 PGA_CEPH-PANEL European 46 IG 1.000 1.000
PGA_YORUB-PANEL Sub-Saharan African 48 IG 0.125 0.875 0.752 0.062 0.938

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.062+/-0.165 199 141 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
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN YES

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Revised: May 25, 2006 1:38 PM .