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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs420613          
refSNP ID: rs420613
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:80/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_002739.3:c.285+2504A>G
NT_011109.15:g.26658191A>G
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 ss12468029 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs420613 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
ss554768SC_JCM|AC008440.5_219702fwd/TA/Gtattttgtatacagtataggttggatccaccaacagcttatttggttatttttccctgtc07/12/0010/10/0380Genomicunknown
ss1121895KWOK|OVLP-000804-319647fwd/TA/Gtattttgtatacagtataggttggatccaccaacagcttatttggttatttttccctgtc09/02/0010/10/0386Genomic99 %
ss12468029WI_SSAHASNP|chr19.NT_011109.15_26658191byFreqfwd/TA/Gtattttgtatacagtataggttggatccaccaacagcttatttggttatttttccctgtc07/04/0310/25/06116Genomicunknown
ss23813144PERLEGEN|afd4635756byFreqfwd/TA/Gtattttgtatacagtataggttggatccaccaacagcttatttggttatttttccctgtc08/10/0409/13/04123Genomicunknown
ss75154870ILLUMINA|ILMN_Human_1M_rs420613fwd/TA/Gtattttgtatacagtataggttggatccaccaacagcttatttggttatttttccctgtc08/28/0708/29/07129Genomicunknown
ss84773284HGSV|Cor18517_SNV_20070510.chr19_59081813fwd/TA/Gtattttgtatacagtataggttggatccaccaacagcttatttggttatttttccctgtc12/06/0712/07/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs420613|allelePos=960|totalLen=2097|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TAGAACATAT ATTGAGCACC ACTGTCTACC AGCACGTGTA TGTGATTGAT GACCCCCCTC
 GTCCACTCAC CTCCGCCACC AACACCAGAT AAGTCTGATG CATCCAGTGC TCATTGGGTA
 CACTCATCAA GATTTTTTTT TTTGTTTTTT gcctgtaatc ccagctactc gggaggctga
 ggcagaattg cttgaacctg agcggcagag gttgcagtga gccaagatca cgccactgca
 ctccagcctg ggtgacagag caagactttg tcttggaaaa aaaaaaaaaG ATTTTTTttt
 gtttttgttg ttttgtttga ttttggggta ttttttagat ggagtttcac tctgtcaccc
 aggctggagt gcactggtgc aatcttggtt cactgcaacc tctacctccc aggttcaagc
 gattctcatg cctcagcctc ccgagtagct gggactagaa caggcatgag ccaccatggc
 cggctaattt ttatattttt agtagacagg gtttcatcat gctggccaag ctggtcttgc
 tcctgacctc acgtgatcca cccacctcgg cctcccaaag tgctgggatt acaggcgtga
 gccaccgcac ccagccGATT TTTGGGGttt tttgagacag ggtcccactc tgtcacctag
 actggagtac agtgatggga tcatagctca ctgcagcctt gaattctcca ggctcaagtg
 ctcctcctgc cccagcttct caagtagctg ggactatagg cacaagccac aacacctagc
 taattaaaaa aaaatgtttt tgtagagatg gagtctcact cactatattg cccaggctgg
 tcttcaactc ctggtctcac tcgattctcc tgcctcagcc tcccaaaatg atgggattac
 aggcgtgagc cactgcacct ggccTCAAGT ATTTTGTATA CAGTATAGGT TGGATCCAC
 R
 CAACAGCTTA TTTGGTTATT TTTCCCTGTc tatctggttt gaatcccagc tccaccactt
 tttggttctg tgacatttcc tgagttaatt tacctctctg cacttgttga attccttgtt
 tgtaaagtgg agatgataat tatgctcact atggattgtt ttgaagattt agtgagtcag
 acatttggga tggtttctga cacatagcaa gagccaaaat attatttttt attCTTGTTA
 AAATTATTAT TATGACCAAT GAGGAAACGA GTGAATAGTG AGAAGGAGAT CTTTCCTCTG
 CATCACTCGG GGGttttttt gtttttgttt ttttttgctg ttgagacagg gtctcactct
 gttgcccagg ctggagtgca atagtgctat cactgctcac tgcagtcttg acctccgggg
 ctcaagtgat tcACTGCTGG CAGTTGATCT TCTTAAAAGT AACATGCAgg ccaggcacag
 tggctcacgc ctgtaatccc aacactttgg gagaccgagg cgggtggatc acctgaggtt
 gggagttcga gaccagcctg accaacatgg agaagccacg tgtctactaa gaatacaaaa
 ttagctgggc gtggtggcac acgcctgtaa tcccagctac tcaggaggct gaggcaggag
 aatcacttga acccaggagg cggaggttgc agtgagccaa gattgcgcca ttgcactcca
 gcctgggcag caagaacaaa actctgtctc aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
 AAAAAAAAGG TAACATGCCT Tgaccaggca tggtggctca tgcctgtaat cccagctctt
 tgggaggctg aggcaagcgg atcacgaggt caggagatcc aaaccatcct ggctaacgcg
 gtgaaacccc gtctctacta aaaatacaaa aaattagcca ggcacggtgg cacgcgcctg
 tagtcccagc tactcgggag gctgaggcag gagtatcgct tgaaccccgg aggcagaggt
 tgcagtgagc cgagatcaca ccactgcact ctagcctggg cgacagagtg agactccatc
 tcaaaaaaaa aaaaaaaaaa aaaGTAACAT GGATCAAGAT TTGGCAAGAA TGATTTC

  GeneView back to top
GeneView via analysis of contig annotation: PRKCG protein kinase C, gamma
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_011109->NM_002739
svfunction
HuRefNW_001838498->NM_002739
svfunction
CeleraNW_927284->NM_002739
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011109->NM_002739->NP_00273026658191forwardintron
HuRefNW_001838498->NM_002739->NP_0027301556708reverseintron
CeleraNW_927284->NM_002739->NP_0027303738326forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs420613 maps exactly once on NCBI human chromosome 19
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
19NW_001838498.2155670850709198minusTalt_assembly_8HuRefHuRefview959
19NW_927284.1373832651431042plusAalt_assembly_1CeleraCeleraview959
19NT_011109.152665819159081813plusAref_assemblyreferencereferenceview959

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011109 AC022318 AC022318.4
dbSNP Blast Analysis
GenBank HTGS Finished:
AC008440.9 NC_000019.8

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss12468029HapMap-CEUEuropean 118IG 0.932 0.068 1.000 0.966 0.034
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 120IG 0.500 0.300 0.200 0.010 0.650 0.350
ss23813144AFD_EUR_PANELEuropean 48IG 1.000 1.000
AFD_AFR_PANELAfrican American 46IG 0.609 0.217 0.174 0.050 0.717 0.283
AFD_CHN_PANELAsian 48IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.189+/-0.24233226090

  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 .