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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs7259278          
refSNP ID: rs7259278
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_000527.2:c.1706-69G>T
NT_011295.10:g.2490268G>T
Links

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 ss69381132 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7259278 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
ss10942642BCM_SSAHASNP|chr19.NT_011295.10_2490268fwd/BG/Tgcagggggtcttcctgcccggagcagcgtgccaggccctcaggaccctctgggactggca06/30/0311/10/03116Genomicunknown
ss22887421IMCJ-GDT|IMCJ-LDLR_17-GTfwd/BG/Tgcagggggtcttcctgcccggagcagcgtgccaggccctcaggncccnctgggactggca03/22/0403/22/04121Genomicunknown
ss23144329PARC|LDLR-029664byFreqfwd/BG/Tgcagggggtcttcctgcccggagcagcgtgccaggccctcaggcccctctgggactggca05/17/0408/05/04126Genomicunknown
ss69381132SI_EXO|NT_011295.10_2490268fwd/BG/Tgcagggggtcttcctgcccggagcagcgtgccaggccctcaggaccctctgggactggca04/12/0704/12/07127Genomicunknown
ss76876894CGM_KYOTO|719230fwd/BG/Tgcagggggtcttcctgcccggagcagcgtgccaggccctcaggaccctctgggactggca09/12/0709/12/07129cDNAunknown
ss84140508PHARMGKB_PARC|PS206655_PA151892228_5911fwd/BG/Tgcagggggtcttcctgcccggagcagcgtgccaggccctcaggcccctctgggactggca12/06/0712/10/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs7259278|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 CTGGCGCAAT CGTAGCTCAC TGCAGCCTCC ACCTCCCAGG CTCAAGTGAT CCTCCTGCCT
 CACCCTCCTG AGTAGCTGAG ATTACAGACA CGTGCCACCA CGGCAGACTA ATTTTATTTT
 ATTTTTGGGA AGAGACAAAG TCTTGTTATG TTGGCCTGGC TGGTCTCAAA CTCAGGGTGC
 AAGCGATCCT CCCGCCTCAG CCTTCCAAAC TGCTGGGATT ACAGGCGTGG GCCACCGTAC
 CCAGCCTCCT TGAAGTTTTT CTGACCTGCA ACTCCCCTAC CTGCCCATTG GAGAGGGCGT
 CACAGGGGAG GGGTTCAGGC TCACATGTGG TTGGAGCTGC CTCTCCAGGT GCTTTTCTGC
 TAGGTCCCTG GCAGGGGGTC TTCCTGCCCG GAGCAGCGTG
 K
 CCAGGCCCTC AGGACCCTCT GGGACTGGCA TCAGCACGTG ACCTCTCCTT ATCCACTTGT
 GTGTCTAGAT CTCCTCAGTG GCCGCCTCTA CTGGGTTGAC TCCAAACTTC ACTCCATCTC
 AAGCATCGAT GTCAACGGGG GCAACCGGAA GACCATCTTG GAGGATGAAA AGAGGCTGGC
 CCACCCCTTC TCCTTGGCCG TCTTTGAGGT GTGGCTTACG TACGAGATGC AAGCACTTAG
 GTGGCGGATA GACACAGACT ATAGATCACT CAAGCCAAGA TGAACGCAGA AAACTGGTTG
 TGACTAGGAG GAGGTCTTAG ACCTGAGTTA TTTCTATTTT CTTCTTTCTT TTTTTTTTTT
 TTTTTGAGAC AGAGTTTTGC TCTCGTTTCC CAGGCTGGAG

  GeneView back to top
GeneView via analysis of contig annotation: LDLR low density lipoprotein receptor (familial hypercholesterolemia)
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_011295->NM_000527
svfunction
HuRefNW_001838483->NM_000527
svfunction
CeleraNW_927195->NM_000527
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011295->NM_000527->NP_0005182490268forwardintron
HuRefNW_001838483->NM_000527->NP_0005183471713reverseintron
CeleraNW_927195->NM_000527->NP_0005182338532forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs7259278 maps exactly once on NCBI human chromosome 19
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
19NW_001838483.2347171310803808minusAalt_assembly_8HuRefHuRefview400
19NT_011295.10249026811088466plusGref_assemblyreferencereferenceview400
19NW_927195.1233853211122286plusGalt_assembly_1CeleraCeleraview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011295.10
dbSNP Blast Analysis
GenBank HTGS Finished:
AC011485.6 NC_000019.8

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceG/G
G/T
T/T
HWPG
T
ss23144329PARC-AFRICAN-PANELAfrican American 48IG 0.375 0.417 0.208 0.527 0.583 0.417
PARC-EUROPEAN-PANELEuropean 44IG 0.864 0.136 0.752 0.932 0.068

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.375+/-0.217472600

  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
UNKNOWNUNKNOWNYES

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Revised: May 25, 2006 1:38 PM .