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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2424558          
refSNP ID: rs2424558
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NT_011387.8:g.23369344A>G
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 ss8360474 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2424558 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
ss3395342SC_JCM|chr_20_23334351fwd/TA/Gtgttccaccttctctttttaatctccccaaaatagtaatgcctgccttggggacaccata09/24/0110/10/03100Genomicunknown
ss8360474SC_SNP|NT_011387.8_23369344fwd/TA/Gtgttccaccttctctttttaatctccccaaaatagtaatgcctgccttggggacaccata04/17/0310/10/03114Genomicunknown
ss20125673CSHL-HAPMAP|CSHL-HuFF-200402.chr20.NT_011387.8_23369344fwd/TA/Gtgttccaccttctctttttaatctccccaaaatagtaatgcctgccttggggacaccata02/21/0403/04/04120Genomicunknown
ss44226660ABI|hCV2522449byFreqfwd/TA/Gtgttccaccttctctttttaatctccccaaaatagtaatgcctgccttggggacaccata07/18/0511/03/06126Genomicunknown
ss78832612HGSV|Cor18507_SNV_20070510.chr20_23377344fwd/TA/Gtgttccaccttctctttttaatctccccaaaatagtaatgcctgccttggggacaccata10/19/0710/20/07129Genomicunknown
ss91670229BCMHGSC_JDW|JWB-1432286fwd/TA/Gtgttccaccttctctttttaatctccccaaaatagtaatgcctgccttggggacaccata02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2424558|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 ACAGGAATGG TGGGCCTGAG CCAGCATTGA GACAGGAGTG GGCACCCAGG CCCTGGCTGA
 GTACAGGGAG GCAGCACAGC AGAGCTCTCC ggcgatggag cagtgctgtg tcttgagcat
 ggtgctggtt acacgaatgt acacgtgtga ctaaaTGGCA CACACACAgt accaatgttg
 gcttcctaat tgtgatattt ttctgtgatg tgataagatg taaccattag gggaaactag
 aggaaggaca cagaggactt ctctctacta cctttgtaac ttcctggaaa tatatactaa
 ttttttaaaa aACTTCAAAG AAAGCCCCCA CAACGTTGGC TGAGAAATCC AAGAGATTAA
 TGGGCATAAA TGTTCCACCT TCTCTTTTTA ATCTCCCCAA
 R
 AATAGTAATG CCTGCCTTGG GGACACCATA GCAAAAAATG TCAGAAAAGT GTTGACTGTT
 GACTGGTATT AAATTACTAC CACTGCCACT GCCAGCATTC TTCCtaatgg ttaatattta
 tttgaatgcc tgcttcgtgt taggcactgt gttaagcaat ttatatgcat tatcatcatc
 aatctttaca actgcctcaa ggagtaggta ctgttattct cagttaaaga tgaagacatt
 gTAGGTTAGC ATCATCCCAG GCAGTTGGCG GAGGGAAACC CCACCTGGGC CCCGCTGAAA
 CAGGGTTCTG GGCATTCCAG CACTTCAACA GGGAGAGTAA AAGCCAAAAA TAAATTATTT
 GTTCTTTCAA AGCCAATCCC ATCTTGGTGA GAACTGGTGT

  GeneView back to top
GeneView via analysis of contig annotation: CST11 cystatin 11
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_011387->NM_080830
function
referenceNT_011387->NM_130794
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011387->NM_080830->NP_54302023369344reverse3' near gene
referenceNT_011387->NM_130794->NP_57061223369344reverse3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2424558 maps exactly once on NCBI human chromosome 20
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
20NT_011387.82336934423377344plusAref_assemblyreferencereferenceview400
20NW_001838653.197543523391006plusAalt_assembly_8HuRefHuRefview400
20NW_927317.12335990023502724plusAalt_assembly_1CeleraCeleraview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011387
dbSNP Blast Analysis
GenBank HTGS Finished:
AL096677.21

  Population Diversity back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceHWPA
G
ss44226660AoD_African_American 90AF 0.070 0.930
AoD_Caucasian 92AF 0.510 0.490

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.414+/-0.1890000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .