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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs17855890          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_013244.2:c.1283G>C
NM_013244.3:c.1283C>G
NP_037376.2:p.Thr428Ser
NT_019546.15:g.9855412G>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 ss48416627 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17855890 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
ss28510192MGC_GENOME_DIFF|BC064141x29802923-G9855412Cfwd/TC/Gccatttttgaattctcctagtcttaagtaatagaacattgtctcctttgtttgctaggca08/25/0408/25/04123cDNAunknown
ss48416627APPLERA_GI|hCV25991474byFreqfwd/C/Gccatttttgaattctcctagtcttaagtaatagaacattgtctcctttgtttgctaggca09/28/0511/03/06126Genomicunknown
ss69115456PERLEGEN|PGP06185959byFreqfwd/C/Gccatttttgaattctcctagtcttaagtaatagaacattgtctcctttgtttgctaggca01/30/0703/31/08127Genomicunknown
ss74910411ILLUMINA|ILMN_Human_1M_rs17855890fwd/C/Gccatttttgaattctcctagtcttaagtaatagaacattgtctcctttgtttgctaggca08/28/0708/29/07129Genomicunknown
ss89294222BCMHGSC_JDW|JWB-0590138fwd/C/Gccatttttgaattctcctagtcttaagtaatagaacattgtctcctttgtttgctaggca02/26/0802/28/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17855890|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=129
 GTCAACAATG TATAAATGAA AACTGCCAAT GTAATTAATG TTTCTTTTAA CATATCCCAT
 CCATTGCTTT CCCTCCAAAA GACAAAGGTA GCAAAAGACG AAGCAGGAAG AACTGCTTCA
 GAAACTGAAC ATACTGATTT AATTGGCTAA GAAGTCCAAA TGCTAATACT CCTAATAATT
 AGCCATTCCT TTTGTGTTTT GGTGACATAT ATCCTCATAC AATGTATATC AAATGGAATT
 TTTTGATTTA CACCTGACAT TTCAAAGTTT CCATTTTTGA ATTCTCCTAG TCTTAAGTAA
 S
 TAGAACATTG TCTCCTTTGT TTGCTAGGCA TAACGTTTTC CCCAACATCT AGGGCTCCAT
 GATGCAAAAT ATCATTTTGC CGATCTTCTG TTCCAGTATT TACTTTAATT TTTTTTATTA
 TAATTGGATT TTCAAATACA ATCACAAAAA CATCTCCTGT TGAAGGTGGT TTCCCCCAAA
 AGTACTCATC AACACTACTG TAAGCCTTGC TTGCTTCATA ATTTTCAAAC ACATTCATGT
 TGGTGTACAG ACTTGCAGGG GGGTTATCAG GAATGTCAAA TGACTCCTCT TCAAAATCAT

  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
NC_000012.9 BC064141
dbSNP Blast Analysis
UniGene Cluster ID
126195

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 G/G
 HWP C
 G
ss48416627 AGI_ASP population multiple 68 IG 0.147 0.853 0.655 0.074 0.926
ss69115456 HapMap-CEU European 120 GF 0.017 0.283 0.700 0.158 0.842
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.094+/-0.195 307 247 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
byClusterbyFreq UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .