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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2425241          
refSNP ID: rs2425241
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:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_014902.3:c.-73+22734T>C
NT_011362.9:g.71327T>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 ss8382316 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2425241 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
ss3396749SC_JCM|chr_20_36720964fwd/BC/Tcatgggtggtggaggctgggctcctggcctctaatgggggaaacagccaggaccacacct09/24/0110/10/03100Genomicunknown
ss8382316SC_SNP|NT_011362.7_71327byFreqfwd/BC/Tcatgggtggtggaggctgggctcctggcctctaatgggggaaacagccaggaccacacct04/17/0310/25/06114Genomicunknown
ss17702548CSHL-HAPMAP|CSHL-HuCC-200402.chr20.NT_011362.8_71327fwd/BC/Tcatgggtggtggaggctgggctcctggcctctaatgggggaaacagccaggaccacacct02/19/0403/04/04120Genomicunknown
ss21801202SSAHASNP|WGSA-200403-chr20.chr20.NT_011362.8_71327fwd/BC/Tcatgggtggtggaggctgggctcctggcctctaatgggggaaacagccaggaccacacct03/20/0403/20/04121Genomicunknown
ss69240554PERLEGEN|PGP05761460byFreqfwd/BC/Tcatgggtggtggaggctgggctcctggcctctaatgggggaaacagccaggaccacacct01/30/0708/14/07127Genomicunknown
ss75117169ILLUMINA|ILMN_Human_1M_rs2425241fwd/BC/Tcatgggtggtggaggctgggctcctggcctctaatgggggaaacagccaggaccacacct08/28/0708/29/07129Genomicunknown
ss80108234HGSV|Cor18507_SNV_20070510.chr20_34451826fwd/BC/Tcatgggtggtggaggctgggctcctggcctctaatgggggaaacagccaggaccacacct11/23/0711/24/07130Genomicunknown
ss91690109BCMHGSC_JDW|JWB-1438717fwd/BC/Tcatgggtggtggaggctgggctcctggcctctaatgggggaaacagccaggaccacacct02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2425241|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTTCTTCCTC TCTCTTTTTA AAAAAAATTA CCTTACATAA GTaagaaaaa taaataagag
 aaaaggagaa aagaaaagac aaaacaagaT GATTCTAGGT TATACTTTAT TAAAGGTAGG
 CTATAAATTT GCCTCTGAGC TTCCTAGTAG ACAAAGAAAA AAAGGAAACA AGAAGTAGCA
 TGATTCACTG TGCCCTTGAA AGGAAAATAA GTCAATTAAT TGCTCAGGTG TGTGCAGAGT
 ATCCATGTCC TCAGAGCCAT TCATACAGTA AATACAGTAA CAACAGGGGC TGCTGCTATG
 ACTCTAGTCC CCAAAGGCTC TGGGGTTCAG AGGGGCCATG ACTGGTACTC TGGAGGCCAT
 GAAACCAAAG CATGGGTGGT GGAGGCTGGG CTCCTGGCCT
 Y
 CTAATGGGGG AAACAGCCAG GACCACACCT ATCCTGCTGC GTGGCAGCAT GGGCTCCAGG
 CTGAAATAGG GGCAGAGAAG TGTGCAAACT GGACCAAGGG GCAGTGAACT TCAGCTGGGA
 GAAGACATCA CAGAAGACAT CATATTTGGC ATAGGCCTTG AAAGCTGAGT AAGGCTCTGA
 CCCCTGGAGA TGACAATGGA GGTCCTGAGT TCCCCATCAG ACCCAGCCTG AGAAGGAGCG
 TCGTCcacag cctgttacag ataaagagag cttagagatt caagttcagc tgcactccca
 tgataggaga actgaggccc agagaaggca gggctaaacc tggagtcaca cagagaggca
 ggaacctagc aggcctcaaa cccaagcctt ctgcctctcT

  GeneView back to top
GeneView via analysis of contig annotation: DLGAP4 discs, large (Drosophila) homolog-associated protein 4
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_011362->NM_014902
svfunction
HuRefNW_001838665->NM_014902
svfunction
CeleraNW_927339->NM_014902
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011362->NM_014902->NP_05571771327forwardintron
HuRefNW_001838665->NM_014902->NP_05571774495forwardintron
CeleraNW_927339->NM_014902->NP_0557175228602forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2425241 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
20NW_927339.1522860231725493plusCalt_assembly_1CeleraCeleraview400
20NW_001838665.17449531754584plusCalt_assembly_8HuRefHuRefview400
20NT_011362.97132734451826plusTref_assemblyreferencereferenceview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011362
dbSNP Blast Analysis
GenBank HTGS Finished:
AL445705.8 NC_000020.9

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss69240554HapMap-CEUEuropean 120GF 0.867 0.133 0.933 0.067
HapMap-HCBAsian 90GF 0.978 0.022 0.989 0.011
HapMap-JPTAsian 90GF 1.000 1.000
HapMap-YRISub-Saharan African 120GF 0.983 0.017 0.992 0.008
ss8382316HapMap-CEUEuropean 120IG 0.867 0.117 0.017 0.251 0.925 0.075
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 118IG 1.000 1.000
Concordant GenotypeTotal SampleC/CC/TT/T
ss6924055426625510
ss838231626625510
RefSNP Genotype SummaryTotal IndividualC/CC/TT/T
rs242524127025610
Discordant Genotypes:
Indiviudal
SampleID		SubSNP(ss)GenotypePopulation
Handle		Submitter
Population		Submitter
SampleID		SampleID
Alias		Submission
Batch		NCBI
ProbeID
264ss8382316T/TCSHL-HAPMAPHapMap-CEUNA11831CEPH1350.12r23_ch20_CEU_perlegen:genotyping_1.0.05748102
264ss69240554C/TCSHL-HAPMAPHapMap-CEUNA11831CEPH1350.12chr20-HapMap-CEU
5175ss8382316C/CCSHL-HAPMAPHapMap-HCBNA18620CH18620r23_ch20_HCB_perlegen:genotyping_1.0.05748102
5175ss69240554C/TCSHL-HAPMAPHapMap-HCBNA18620CH18620chr20-HapMap-HCB
5251ss8382316C/CCSHL-HAPMAPHapMap-YRINA18523YOR016.02r23_ch20_YRI_perlegen:genotyping_1.0.05748102
5251ss69240554C/TCSHL-HAPMAPHapMap-YRINA18523YOR016.02chr20-HapMap-YRI
5283ss8382316C/CCSHL-HAPMAPHapMap-YRINA19205YOR048.01r23_ch20_YRI_perlegen:genotyping_1.0.05748102
5283ss69240554C/TCSHL-HAPMAPHapMap-YRINA19205YOR048.01chr20-HapMap-YRI
Genotype data submitted for270 samples from270 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .