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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2232842          
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:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_016243.2:c.131A>G
NP_057327.2:p.Asn44Ser
NT_004487.18:g.53426265T>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 ss48401379 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2232842 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
ss3180202GENAISSANCE|GEN1885fwd/TA/Ggccggcctcaggtcactctcctggaccccatgaaaagtacctgctacgactgctagacaa07/19/0110/10/0398Genomicunknown
ss16240837CGAP-GAI|1478819fwd/TA/Ggccggcctcaggtcactctcctggaccccatgaaaagtacctgctacgactgctagacaa11/18/0311/22/03120cDNAunknown
ss48401379APPLERA_GI|hCV15944095byFreqrev/BC/Tttgtctagcagtcgtagcaggtacttttcatggggtccaggagagtgacctgaggccggc09/28/0511/03/06126Genomicunknown
ss74911497ILLUMINA|ILMN_Human_1M_rs2232842fwd/TA/Ggccggcctcaggtcactctcctggaccccatgaaaagtacctgctacgactgctagacaa08/28/0708/29/07129Genomicunknown
ss81544101HGSV|Cor18956_SNV_20070510.chr1_199667568rev/BC/Tttgtctagcagtcgtagcaggtacttttcatggggtccaggagagtgacctgaggccggc11/30/0711/30/07130Genomicunknown
ss106625476BGI|BGI_rs2232842rev/BC/Tttgtctagcagtcgtagcaggtacttttcatggggtccaggagagtgacctgaggccggc09/16/0806/16/09130Genomicunknown
ss1088733321000GENOMES|CEU.trio.12.15.2008_229034_chr1_201202534rev/BC/Tttgtctagcagtcgtagcaggtacttttcatggggtccaggagagtgacctgaggccggc12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2232842|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 CTGGGCCCAC CGTGGATGCT GGGGTCCCGA TCCCGCACAT CCGGGCTCGG GACTCCGCCA
 GGTTACCCCT CTGCCCTTGG CATGCCTCCG CGCTGGAGCT CGGGATCGCC ACCCCTGGGA
 CGGTCACCAC CCAAGCCCCG GGCTCTTACC CAGCCTGGCG GTCACGCTGC CTCCTCTACC
 CACAGAGCCC CGTCCTGCTG GCCTCCCTGG GGGTGGGGCT GGTCACTCTG CTCGGCCTGG
 CTGTGGGCTC CTACTTGGTT CGGAGGTCCC GCCGGCCTCA GGTCACTCTC CTGGACCCCA
 R
 TGAAAAGTAC CTGCTACGAC TGCTAGACAA GACGGTAAGT TGGGGAAGAA AGGGCCAGGG
 TGAAGGAGGG GACCAGAGTG CTCCTGGCAT GGAGGGTACA GCACCCACGG TGGTTGGGAT
 GTCCAAGGGA CGTGGCAGCG CCAGGCGCGC TTGGTGAAAC ACTTGTGTCC TCCACCCTCC
 AGACTGTGAG CCACAACACC AAGAGGTTCC GCTTTGCCCT GCCCACCGCC CACCACACTC
 TGGGGCTGCC TGTGGGTAAG GAAAGTGTGG AATGGGCTCC TTTCCCTGGT ATCCTCAGAA

  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
BE880218 BM045763
dbSNP Blast Analysis
UniGene Cluster ID
334832

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss48401379 HapMap-CEU European 120 IG 0.983 0.017 1.000 0.992 0.008
HapMap-HCB Asian 90 IG 0.289 0.578 0.133 0.251 0.578 0.422
HapMap-JPT Asian 88 IG 0.364 0.477 0.159 1.000 0.602 0.398
HapMap-YRI Sub-Saharan African 120 IG 0.717 0.267 0.017 0.752 0.850 0.150
AGI_ASP population multiple 74 IG 0.892 0.108 0.752 0.946 0.054

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.314+/-0.242 1245 1040 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 .