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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2242090          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:98/130
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_023078.2:c.486G>C
NP_075566.2:p.Lys162Asn
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 ss43243782 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2242090 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
ss3198259YUSUKE|IMS-JST014181byFreqfwd/TC/Ggggccgccacgtggggagcagcgagaccaactcctgcagcatctgctggaggcctgtggg08/07/0110/10/0398Genomicunknown
ss16249693CGAP-GAI|1498449fwd/TC/Ggggccgccacgtggggagcagcgagaccaactcctgcagcatctgctggaggcctgtggg11/18/0311/22/03120cDNAunknown
ss17242846CSHL-HAPMAP|CSHL-HuAA-200402.chr8.NT_023684.16_621579rev/BC/Gcccacaggcctccagcagatgctgcaggagttggtctcgctgctccccacgtggcggccc02/17/0403/04/04120Genomicunknown
ss22761346SSAHASNP|WGSA-200403-chr8.chr8.NT_023684.16_621579rev/BC/Gcccacaggcctccagcagatgctgcaggagttggtctcgctgctccccacgtggcggccc03/21/0403/21/04121Genomicunknown
ss28497529MGC_GENOME_DIFF|37552441-C621579Grev/BC/Gcccacaggcctccagcagatgctgcaggagttggtctcgctgctccccacgtggcggccc08/20/0408/20/04126cDNAunknown
ss28512249MGC_GENOME_DIFF|BC007993x37552441-C621579Grev/BC/Gcccacaggcctccagcagatgctgcaggagttggtctcgctgctccccacgtggcggccc08/25/0408/25/04126cDNAunknown
ss43243782ABI|hCV16173479rev/C/Gcccacaggcctccagcagatgctgcaggagttggtctcgctgctccccacgtggcggccc07/18/0507/18/05126Genomicunknown
ss48426413APPLERA_GI|hCV16173479byFreqfwd/C/Ggggccgccacgtggggagcagcgagaccaactcctgcagcatctgctggaggcctgtggg09/28/0511/03/06126Genomicunknown
ss93989318BCMHGSC_JDW|JWB-2541562rev/C/Gcccacaggcctccagcagatgctgcaggagttggtctcgctgctccccacgtggcggccc02/26/0803/05/08129Genomicunknown
ss97911708HUMANGENOME_JCVI|1103652471365rev/C/Gcccacaggcctccagcagatgctgcaggagttggtctcgctgctccccacgtggcggccc03/30/0803/30/08130Genomicunknown
ss1084989401000GENOMES|CEU.trio.12.15.2008_2107819_chr8_144759879rev/C/Gcccacaggcctccagcagatgctgcaggagttggtctcgctgctccccacgtggcggccc12/15/0812/15/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2242090|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 AGAGGTGGCC GTGTGGCCCA CCTGGATCAA GTGGCTGGAT TTAGGGTTCC CTCCTGGTGC
 TGTACCTGGG AGGCAGACGC TGGAGCCCAC CGCGAGCTGA CGTGGACCTT TCCTGAGGCC
 CCTGCTGGGG CCTGCCCAGC AGGGCCCAGT CCTACAGACT CCCTGATTCT GACCTCTCTC
 TGGCCAGCTG CTGCCCCCAA ACACACGGGT GCTGCGGGTC TTGCCCAACC TGCCCTGTGT
 GGTCCAGGAA GGGGCCATAG TGATGGCGCG GGGCCGCCAC GTGGGGAGCA GCGAGACCAA
 S
 CTCCTGCAGC ATCTGCTGGA GGCCTGTGGG CGGTGTGAGG AGGTGCCTGA AGCCTACGTC
 GACATCCACA CTGGCCTCAG TGGCAGTGGC GTGGCCTTCG TGAGTATTGC CTCGTCCATC
 CCCGGCCCCA CCCTCGGCAA AGAGGGGGCC CACCCCAGTC CCTCTGACAG CCTCTGCCCT
 CAGAGTCCAA CCTTGAGGCC TGCGTGGTTG CTCCCCAGGC CCACTGGGAG CTCTGCTTGT
 CCCCGGGACT TCACTGCCTT GGGGATCTTT GAGGCCAGCC CCTTTGCAGA CCGTTGGGCT

  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_023684 ABBA01005246 BC007993 BM548059
dbSNP Blast Analysis
UniGene Cluster ID
165186

  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
ss3198259 JBIC-allele 1496 AF 0.358 0.642
ss48426413 AGI_ASP population multiple 58 IG 0.138 0.310 0.552 0.200 0.293 0.707

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.414+/-0.188 35 34 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
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .