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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1358786          
refSNP ID: rs1358786
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_006661.1:c.-92+20513T>C
NT_007422.13:g.8342263A>G
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 ss5477218 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1358786 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
ss2140990TSC-CSHL|TSC0498328fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta10/19/0010/10/0388Genomic95 %
ss4233701SC_JCM|AL591962.10_61920fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta10/15/0110/10/03101Genomicunknown
ss5477218TSC-CSHL|TSC0900801byFreqfwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta09/21/0204/07/04108Genomicunknown
ss5958468SC_JCM|NT_007422.10_4983854fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta01/10/0310/10/03111Genomicunknown
ss20264076CSHL-HAPMAP|CSHL-HuFF-200402.chr6.NT_007422.12_8342263fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta02/21/0403/04/04120Genomicunknown
ss22391448SSAHASNP|WGSA-200403-chr6.chr6.NT_007422.12_8342263fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta03/21/0403/21/04121Genomicunknown
ss66671160ILLUMINA|HumanHap300v1.1_rs1358786fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta11/09/0611/09/06127Genomicunknown
ss67085377ILLUMINA|HumanHap550v1.1_rs1358786fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta11/14/0611/14/06127Genomicunknown
ss67418596ILLUMINA|HumanHap650Yv1.0_rs1358786fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta11/14/0611/14/06127Genomicunknown
ss70425878ILLUMINA|HumanHap300v2.0_rs1358786fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta04/18/0711/18/07127Genomicunknown
ss70608411ILLUMINA|HumanHap550v3.0__rs1358786rev/BC/Ttagttcagacatcaacctttaaaacatgtggatgccttctcttcttagatatagtgttgt04/20/0703/30/08130Genomicunknown
ss71155526ILLUMINA|HumanHap650Yv3.0_rs1358786fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta04/23/0704/23/07127Genomicunknown
ss74846178AFFY|SNP_M-605063fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta08/09/0708/09/07128Genomicunknown
ss75596650ILLUMINA|ILMN_Human_1M_rs1358786fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta08/28/0708/29/07129Genomicunknown
ss79793901HGSV|Cor18507_SNV_20070510.chr6_166025333fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta11/23/0711/23/07130Genomicunknown
ss83736151KRIBB_YJKIM|KHS531054fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta12/04/0712/05/07130Genomicunknown
ss93602237BCMHGSC_JDW|JWB-2251829fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta02/26/0803/04/08129Genomicunknown
ss1112991591000GENOMES|CEU.trio.12.15.2008_1672901_chr6_165974912fwd/TA/Gacaacactatatctaagaagagaaggcatccacatgttttaaaggttgatgtctgaacta12/15/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1358786|allelePos=139|totalLen=648|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 AATTATAGCA GCAAACAGAA CTGTAAACCT CAAGAGTCCT TTAAAATACA TTTCTCTACT
 ATAAAACAAT AATAACTGAT GCTCATAAAA AGGTAAAATA TCAGATGCAC AACACTATAT
 CTAAGAAGAG AAGGCATC
 R
 CACATGTTTT AAAGGTTGAT GTCTGAACTA ACTGAAATCA CTAAAAACAG GTGCTTTAAA
 AGTTACACTT CAGTAATCTG GCAAATGCTT CCCCAGCAAT GCTGGCTCTC AGAGGCAGAG
 GTGGTGCCTC ACCCATGATA ACCCACAGTC AGAGCGGGCA CTGGCCACTC AGCTAATATT
 GGCAAATATT ATTTAGAGTG CCTTGGGGGC AGGCCCTCCA CTGAGACCCT GAGCACAGCT
 AAGGCAAAGC AGCCTGGCTC CTCCCTCACT GCACCCACCG TGTGGTGATT CAAGTCTGTT
 CCTAGATGCC CTAGATGTTC CTGAGCCTCA CTTTGCTTAG GATTCCTCTT CGGACTGTTA
 TGAGAACCAA GGAAGATGAG GAATAGAAAG CAATCTTTGA AACAGAACAC GGTCCCGTCT
 CTGGCAAGCG GTGTTTCGGT TCATCTCAAC TCTCCAGCCA CCCTGTACCT CCCACGGCAG
 CCCCGCAGCC TCTGTCCTGC AGGCCACCA

  GeneView back to top
GeneView via analysis of contig annotation: PDE10A phosphodiesterase 10A
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_007422->NM_006661
svfunction
HuRefNW_001838992->NM_006661
svfunction
CeleraNW_923184->NM_006661
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_007422->NM_006661->NP_0066528342263reverseintron
HuRefNW_001838992->NM_006661->NP_006652654269forwardintron
CeleraNW_923184->NM_006661->NP_00665298862216reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1358786 maps exactly once on NCBI human chromosome 6
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
6NW_001838992.2654269163516960minusCalt_assembly_8HuRefHuRefview138
6NT_007422.138342263165974912plusAref_assemblyreferencereferenceview138
6NW_923184.198862216166793612plusGalt_assembly_1CeleraCeleraview138

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007422.10 AL121789
dbSNP Blast Analysis
GenBank HTGS Finished:
AL121789.38

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss5477218CEPH 184AF 0.320 0.680
HapMap-CEUEuropean 120IG 0.050 0.183 0.767 0.100 0.142 0.858
HapMap-HCBAsian 90IG 0.022 0.156 0.822 0.371 0.100 0.900
HapMap-JPTAsian 88IG 0.136 0.864 0.655 0.068 0.932
HapMap-YRISub-Saharan African 120IG 0.133 0.400 0.467 0.439 0.333 0.667

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.285+/-0.24827021000

  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: ILLUMINA
DoubleHit found by:  BCM_SSAHASNP, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .