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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1946940          
refSNP ID: rs1946940
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:92/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_003909.2:c.733-540C>A
NT_008046.15:g.776396C>A
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 ss2840450 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1946940 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
ss2840450TSC-CSHL|TSC1021955byFreqfwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat01/03/0105/17/0492Genomicunknown
ss5907567SC_JCM|NT_023717.9_16769fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat01/10/0310/10/03111Genomicunknown
ss11921288WI_SSAHASNP|chr8.NT_008046.13_776396fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat07/04/0310/10/03116Genomicunknown
ss17968925CSHL-HAPMAP|CSHL-HuCC-200402.chr8.NT_008046.14_776396fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat02/19/0403/04/04120Genomicunknown
ss22703494SSAHASNP|WGSA-200403-chr8.chr8.NT_008046.14_776396fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat03/21/0403/21/04121Genomicunknown
ss44912000ABI|hCV2176058fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat07/19/0507/19/05126Genomicunknown
ss66773743ILLUMINA|HumanHap300v1.1_rs1946940fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat11/09/0611/09/06127Genomicunknown
ss67209416ILLUMINA|HumanHap550v1.1_rs1946940fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat11/14/0611/14/06127Genomicunknown
ss67602357ILLUMINA|HumanHap650Yv1.0_rs1946940fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat11/14/0611/14/06127Genomicunknown
ss70687671ILLUMINA|HumanHap550v3.0__rs1946940fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat04/20/0703/30/08130Genomicunknown
ss71252226ILLUMINA|HumanHap650Yv3.0_rs1946940fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat04/23/0704/23/07127Genomicunknown
ss75788641ILLUMINA|ILMN_Human_1M_rs1946940fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat08/28/0708/29/07129Genomicunknown
ss78337460HGSV|Cor12878_SNV_20070510.chr8_87627399fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat10/17/0710/19/07129Genomicunknown
ss79103119ILLUMINA|HumanHap300v2.0_rs1946940fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat04/18/0711/18/07130Genomicunknown
ss79843846HGSV|Cor18507_SNV_20070510.chr8_87627399fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat11/23/0711/23/07130Genomicunknown
ss83925663KRIBB_YJKIM|KHS574640fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat12/04/0712/06/07130Genomicunknown
ss93922624BCMHGSC_JDW|JWB-2491215fwd/TA/Cgatcattcttttgggggaaggaaatataaaaagaggaggtgttagatcaatttttaacat02/26/0803/05/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1946940|allelePos=245|totalLen=609|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 TATAAGTTGG AGGTGATTAT AATGTCACTG TGAAGAAAAA ATTAAATGAG ACACTTGAAA
 ATAACACAGA GTATGTAACT AAATTTCATA TAGTTGTAGA AATTTAAAGA GGTAGATAGA
 GATCAGAGAA GACTAGAGTA GCAGTGGAAG TTACAGAGGA GAACAACTTG AGCCAAGCCC
 TAAAGATGGA TAGGGGGATA GGAAGGGGAA GGAAGATCAT TCTTTTGGGG GAAGGAAATA
 TAAA
 M
 AAGAGGAGGT GTTAGATCAA TTTTTAACAT GTATTCCCAG TGGAAAGAGA AGATCTTTGA
 TGCATATTTT ACCATAGAGT TGGGCTTCAT ATATTTGTTT TATGATGTTA TTTTTTTTTC
 TTTTCTTTGC AGCATATTTT CGTTCTTTAT GTTGGTAACA GCTAGGAGTA ATATTTTATT
 TCCTTTATTA TACCATGTTA TATCATAGGG CCCAACTCTA TGGTAAAATA TGCAGCAAAG
 AGAAAAAAGA TTATGCCTTG GAACATTTGC AAGGAAATTA CCTGCAGAGG TAAAATTTAT
 TTGGGAGAAA TATTTTGAAA GGTATGCAAT TTTAGGAGTG CCTTAATTGT TGGAAATTTA
 CCTG

  GeneView back to top
GeneView via analysis of contig annotation: CPNE3 copine III
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_008046->NM_003909
svfunction
HuRefNW_001839136->NM_003909
svfunction
CeleraNW_923984->NM_003909
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_008046->NM_003909->NP_003900776396forwardintron
HuRefNW_001839136->NM_003909->NP_003900709220forwardintron
CeleraNW_923984->NM_003909->NP_003900718154forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1946940 maps exactly once on NCBI human chromosome 8
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
8NW_001839136.170922082767696plusCalt_assembly_8HuRefHuRefview244
8NW_923984.171815483752836plusCalt_assembly_1CeleraCeleraview244
8NT_008046.1577639687627399plusCref_assemblyreferencereferenceview244

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023717.9
dbSNP Blast Analysis
GenBank HTGS Finished:
AC013751.6 AC103817.6 NC_000008.9

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/C
C/C
HWPA
C
ss2840450HapMap-CEUEuropean 120IG 0.200 0.600 0.200 0.150 0.500 0.500
HapMap-HCBAsian 90IG 0.178 0.556 0.267 0.439 0.456 0.544
HapMap-JPTAsian 86IG 0.163 0.442 0.395 0.752 0.384 0.616
HapMap-YRISub-Saharan African 120IG 0.317 0.500 0.183 1.000 0.567 0.433

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.500+/-0.01427021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .