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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1288362          
refSNP ID: rs1288362
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/129
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_001007099.1:c.257-93T>C
NM_001007100.1:c.248-93T>C
NM_001007250.1:c.127-93T>C
NM_002979.3:c.1469-93T>C
NT_032977.8:g.23485356T>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 ss2032278 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1288362 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
ss2032278KWOK|OVLP-000925-698116byFreqfwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa10/06/0010/25/0687Genomic99 %
ss2433271SC_JCM|AL358233.3_51126rev/TA/Gttgtcaagagccactgactgcaacagaatttaaccagcactgaggcagtgtggggaaatg11/03/0010/10/0392Genomicunknown
ss19152534CSHL-HAPMAP|CSHL-HuDD-200402.chr1.NT_032977.6_15076508fwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa02/20/0403/04/04120Genomicunknown
ss24238750PERLEGEN|afd1031485byFreqfwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa08/10/0409/13/04123Genomicunknown
ss44127774ABI|hCV7842838byFreqfwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa07/18/0511/03/06126Genomicunknown
ss68765823PERLEGEN|PGP01031485byFreqfwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa01/30/0708/14/07127Genomicunknown
ss75057390ILLUMINA|ILMN_Human_1M_rs1288362fwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa08/28/0708/29/07129Genomicunknown
ss76889898SI_EXO|NT_032977.8_23485356fwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa09/20/0709/20/07129Genomicunknown
ss78717635HGSV|Cor12878_SNV_20070510.chr1_53225458fwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa10/17/0710/20/07129Genomicunknown
ss87425492BCMHGSC_JDW|JWB-0045128fwd/BC/Tcatttccccacactgcctcagtgctggttaaattctgttgcagtcagtggctcttgacaa02/26/0802/26/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1288362|allelePos=2862|totalLen=3062|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTTTGTATTA TTAAAATTGC ATACACTTGA TTTTAAAAAA TTAGAAAAGA TAGACAAACG
 AAACGAAGAA CTACCCTACC AAAATTCCAC TGTCCAGGTT AGGAGTTGGC AAATTATGGC
 CTGCAGACCA AATCTAGCCC ATCACCTGTT TTTTTGTTTT GCGTTTTGTA AAATTTTTGT
 TGAAGTCTAG CCTGTagtaa agggcgtaat tccagagtgt accacgtgat gaatgtttac
 aaatgagtac acctccaagg tcaagacaca gaatgttgcc agtactccag aagcctccct
 cctgcccccc tgctatcact attcactccc aaaaggaacc attatttcaa atcctatcac
 catagcttga ttttatttat tttagaaatt catacaaatg gaaccataga acaataacat
 ttactctttt ttaggtctgg cttttttttg ttcaacagca taagattcat tcatatggtt
 gcgtgtggca atagttTGTG TTTACTAGGC GAATACCCCA GAATTTATTC CTTGTGCATT
 TGATGTATCT TTGCATTGTT TCAATCTGGG AGCCTGATGA ATAAAGTTGT TATGAATATT
 CTTATAGATG TCTTTTAGTG GACATTTCCA TCGTACTTAC TTCTACTGGA CACGCACCCA
 GGGCTAGGTG ATAAAGTGCA GGTTTTGGGT ATGGATGTAC TATTTTACAT TTCCTTCCAT
 ATTACATGAG AGTTTTAGTT CCTCCACATT TTTGACAGTA CTTGGTACTT GCCAGGTTTT
 TTTAAAAATC AGGTTAAttg atgtacaatt aacaataaac aataaaatca acccttttta
 gatgtataat tctgtgaatt tagacaaatg catacagttg tgtaactatc accagaaatc
 aagatacaga cagtttccat taccccagaa agtgtcctca tgtccctcta tagtcagccc
 cctcaggccc ttttagccac tagtttgatt tctctccctg tagttttgct ttccttagga
 agtcatacac atgaaatgat acagtatgta gctttttgag cctccttctt tcactgaaat
 ttattcatgc tgttgcatgg atcatgaagt attttattct tttttgctgc tgaatggtta
 ccccttcacc agttgatgca catttgggtt ttttccagct tttggcaagt atgaatctta
 aagccactat aagcattcac atacaggttt ttgtgtggac gtaagttttc atttttcttc
 ggtaaatacc taggaatagg attgctagtt catatagtat gtgtatgttt agctttatgt
 gaaacttcca gactgttttc tgaaagtggc tgcatcattt tacagtcttt ctggtattat
 gttgaccttt catttgtttc ccatcctcac taacactggg tattgtcttt tttttttttt
 ttttaaattt cagccatttg ttctagtagg tatgtggcac tcatcatgat tttaatgtga
 attttctgat gattaatgaa gtgaagcact gtttcatgtg tttcttggcc atttggagat
 cttcttttat ataatgccta catgtgtcat ttgctcattt ttatattgga tcgtctaacc
 ttttctagtt gagcagtagg agttctttTT TTTATCTTTT CCTGTAATCC ACTGTACCTT
 AGAAaggatt tcttcatata gtctgtatat gagttgtttg tcagagatat atgagttgca
 aatatcttct ccTCCCTCTg tctgccacct gtttaaaata attttattgg aacatagcca
 acatttgttt atatattatc tatgactgct tttgcactac aggggcagaa ttgggtagtt
 gtgatagaga cctactgacc tgcaaagcct aaaatattta gtgtctgatc tgttacagaa
 agtttgttaa cccttgATCT AGAGAACCgt attcattttc tattactgca taacaaattg
 ccacaaattt agtagcttaa aacaatgccc acatttatta gcccacagtt tccatggata
 agtaggctga ggacagctta gctgggtcct ctgcatagag tcacacaagg ctacagttaa
 gcttttggcc agggctgggc tctcatctgg aggcttcaat ggggaaggat ccatgtccaa
 gttcattcag gttgctggca gaattcattt ccctgtggcc ttgggaatga tagcttccct
 cttttactgg ctataggcca gagctggccc tcagctccta acggccagtt ccctgccacg
 tggccctctc cataggaagt ccacaacata gcagtgagct cattcagagc cagcaggaga
 gcaagaatga gtctgctagc aaggtagaat catttaatgt aacaaaatga caagagtgac
 atctcattat ctttgccata ttctgttagc tagaagcaag tcacaggttc tactcacact
 ggaaggaagg ggatgtacac caggaggGTC ACCTTAGAGT CTGTCACAGT TACTATTAGT
 AATATATTGG TGTCTTAAGT TTACAGATGT TTTTCTATGT TTATATAGTT GAATTCTGTT
 TTAAGCAAaa atggcatcat acagtttctt ttgtaactgg cttatataat aatatcatga
 ataatgtaac atgaacattt tttcatgtca gtaaatccag atccatatca tttcttattg
 tggcttgtat catacctcac tatttgaata taccataatt tatttaatca attccgtctt
 gttaaatatc aggattgctt gtggtttATG TCACATTTTA CCAGGCTGCC ATAGAAGTAT
 ATGTGAGTGC CCATTTCCCC ACACTGCCTC AGTGCTGGTT A
 Y
 AATTCTGTTG CAGTCAGTGG CTCTTGACAA AAATGTATAT GTGAAACTGA ACACCTCCTA
 TTCTCCTTCC TTCTCCTGTG TATCTGTTTT AGATAAGAAG GCTGACTGCA CAATCACAAT
 GGCTGACTCA GACTTCCTGG CTTTAATGAC TGGTAAAATG AATCCTCAGT CGGTAAGTAT
 GATGGAGCTT ATATCCTGCT

  GeneView back to top
GeneView via analysis of contig annotation: SCP2 sterol carrier protein 2
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_032977->NM_001007099
function
referenceNT_032977->NM_001007100
function
referenceNT_032977->NM_001007250
function
referenceNT_032977->NM_002979
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_032977->NM_001007099->NP_00100710023485356forwardintron
referenceNT_032977->NM_001007100->NP_00100710123485356forwardintron
referenceNT_032977->NM_001007250->NP_00100725123485356forwardintron
referenceNT_032977->NM_002979->NP_00297023485356forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1288362 maps exactly once on NCBI human chromosome 1
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
1NW_001838579.23016580251628920minusAalt_assembly_8HuRefHuRefview2861
1NW_921351.12766227051801412plusTalt_assembly_1CeleraCeleraview2861
1NT_032977.82348535653286025plusTref_assemblyreferencereferenceview2861

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_032977.8 AC022728 AL358233.3
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL445183.19 AL358233.3

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss2032278HapMap-CEUEuropean 120IG 0.167 0.467 0.367 1.000 0.400 0.600
HapMap-HCBAsian 90IG 0.489 0.511 0.050 0.244 0.756
HapMap-JPTAsian 88IG 0.114 0.432 0.455 1.000 0.330 0.670
HapMap-YRISub-Saharan African 120IG 0.033 0.967 1.000 0.017 0.983
CHMJAsian 74IG 0.284 0.716
ss24238750AFD_EUR_PANELEuropean 48IG 0.125 0.625 0.250 0.200 0.438 0.562
AFD_AFR_PANELAfrican American 46IG 0.043 0.304 0.652 1.000 0.196 0.804
AFD_CHN_PANELAsian 48IG 0.042 0.333 0.625 1.000 0.208 0.792
ss44127774AoD_African_American 90AF 0.140 0.860
AoD_Caucasian 92AF 0.380 0.620
AoD_Chinese 90AF 0.230 0.770
AoD_Japanese 90AF 0.200 0.800
ss68765823HapMap-CEUEuropean 120GF 0.167 0.467 0.367 0.400 0.600
HapMap-HCBAsian 90GF 0.489 0.511 0.244 0.756
HapMap-JPTAsian 90GF 0.111 0.444 0.444 0.333 0.667
HapMap-YRISub-Saharan African 120GF 0.033 0.967 0.017 0.983

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.373+/-0.2183322602700

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .