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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs9660040          
refSNP ID: rs9660040
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:C
Clinical Association:unknown
HGVS Names
NM_016361.3:c.781-374A>G
NT_034400.4:g.665343T>C
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 ss13454851 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9660040 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
ss13454851WI_SSAHASNP|chr1.NT_034400.2_687961fwd/BC/Tcgatctcggctcactgcaagctccacctccgggttcacgccattttcctgtctcagcctc10/31/0311/10/03119Genomicunknown
ss84707133HGSV|Cor19129_SNV_20070510.chr1_144349542fwd/BC/Tcgatctcggctcactgcaagctccacctccgggttcacgccattttcctgtctcagcctc12/06/0712/07/07130Genomicunknown
ss87806304BCMHGSC_JDW|JWB-0122090fwd/BC/Tcgatctcggctcactgcaagctccacctccgggttcacgccattttcctgtctcagcctc02/26/0802/26/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9660040|allelePos=301|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GGAACCTGCA GGAGCCCATC TTCTCCTGGG GAAGAGAAGA CAGGCTCAAG AACAGCTATG
 TCTGTTAACA GGTCAAGAAG CTATGTCTCT AAAGCTCTTC CAAAGCTATT ACTAGATACC
 TGAAGGCCAG GAAAAAAAAA AAAAAAGAAA GGGTTTCTTC CCTTTCTGAT GACTCCCCAT
 CCACTCAAAA ATGAAAAGCA tttttgttgt ttttttggtt ttttttgaga cggagtcccg
 ctctgtcgcc caggctggag tgcagtggca cgatctcggc tcactgcaag ctccacctcc
 Y
 gggttcacgc cattttcctg tctcagcctc ctgagtagct gggactacag gtgcccgcca
 ccacgcccgg ctaatttttt tgtattttta gtagagacgg ggtttcaccg tgttagccag
 gatggtctca atctcctgac ctcgtgatcc acccttctcg gcctcccaaa ttgctgggat
 tacaggtgtg agccaccgcg cctggccTGT TTTACTGGtt tttttttttt tgagatggag
 tcttgccctg tcacccaggt tggaatgcag tggcgtgatc tcggctcact gcaagctcca
 cctcccgctt tcacgccatt ttcctgtctc agcctcctga gtagctggga ctacaggtgc
 ccgccaccac gcccggctaa tttttttgta tttttagtag agacggggtt tcaccgtgtt
 agccaggatg gtctcaatct cctgacctcg tgatccaccc ttctcggcct cccaaattgc
 tgggattaca ggtgtgagcc

  GeneView back to top
GeneView via analysis of contig annotation: ACP6 acid phosphatase 6, lysophosphatidic
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_034400->NM_016361
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_034400->NM_016361->NP_057445665343reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs9660040 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_001838511.1654162120538324plusCalt_assembly_8HuRefHuRefview300
1NW_924906.1275665121859272minusGalt_assembly_1CeleraCeleraview300
1NT_034400.4665343145591350plusTref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_034400
dbSNP Blast Analysis
GenBank HTGS Finished:
AL359207.7

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
with2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .