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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs10180872          
refSNP ID: rs10180872
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_001002257.1:c.-4-9117C>T
NM_182551.3:c.111-9117C>T
NT_022184.14:g.9555269C>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 ss14044459 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10180872 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
ss14044459WUGSC_SSAHASNP|chr2.NT_022184.13_9555269byFreqfwd/BC/Ttcaggctagaggcttgccattgtttctgcgggctaagtgcatgcattcatcctagtagag11/05/0310/25/06119Genomicunknown
ss91103868BCMHGSC_JDW|JWB-1218762fwd/BC/Ttcaggctagaggcttgccattgtttctgcgggctaagtgcatgcattcatcctagtagag02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10180872|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 tggatttcct aggccgacta agaattccta accctagctg gggaaggtga ctgtatccac
 ctttaaatat ggggcttgta actcagctca cacctgacca atcaggtaac agagagctca
 ctaaaatacc cgttaagcta aaagcaggag gtaaagaaat agtcatctat cgcctgagag
 cacaggggga gggacaacta tcaggatata aacctaggta ttcgaactgg cagtggcaac
 cccctttgga tcccctccca ttgtatggga gctttgtttt cactctatta aatcttgcaa
 ctgcacactc ttctggtcca tgtttgttag ggctcaagct gagctttcac tcgccgtcca
 ccactgctga acgtcgccgt cgcagacccg ccattgactt tcaccgctct ggatccggca
 aggtgtctgc tgcgcttctg atgcagcaag gcgcccattg ccgctcctga tcaggctaga
 ggcttgccat tgtttctgcg
 Y
 ggctaagtgc atgcattcat cctagtagag ctgaacacta gtcgctgggt tccacggttc
 tgttctgtga cccacggctt ctaacagagc tataacactc ccctcgtggc ccaaggttcc
 attccttgga atccttgagg ccaagaaccc caggtcagag agcaaaaggc ttgctgctat
 cttgggagca gcctgccatc atcttgagag cTCTAAGAAC AAAGACCCAC CAGTAACATC
 TGGTGGCCTG TACagggatt ctccaaagcc ctgagtaata ctggaccact ttgacttgct
 attctgtcct atccttcctt agaatcagag gaaaatactg ggcagctgtt gaccatttaa
 aaatgattag catggctgct ggacttaaga ctcaggtgtg aggctttctg ggaaaaggcg
 aacagccccc atctgagttg ggagcattgg tctgcctgga accagcttcc gcttttacaa
 ttttcctggg gaagctgagg

  GeneView back to top
GeneView via analysis of contig annotation: LYCAT lysocardiolipin acyltransferase 1
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_022184->NM_001002257
function
referenceNT_022184->NM_182551
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_022184->NM_001002257->NP_0010022579555269forwardintron
referenceNT_022184->NM_182551->NP_8723579555269forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs10180872 maps exactly once on NCBI human chromosome 2
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
2NW_001838769.157360530477361plusCalt_assembly_8HuRefHuRefview500
2NW_927719.13051437130582436plusCalt_assembly_1CeleraCeleraview500
2NT_022184.14955526930592840plusCref_assemblyreferencereferenceview500
7NT_079596.233650580133615012plusTalt_assembly_2CRA_TCAGchr7v2CRA_TCAGchr7v2view500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022184
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss14044459HapMap-CEUEuropean 118IG 0.492 0.424 0.085 1.000 0.703 0.297
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 88IG 0.955 0.045 1.000 0.977 0.023
HapMap-YRISub-Saharan African 104IG 0.731 0.269 0.273 0.865 0.135

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.222+/-0.24827021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .