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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1358782          
refSNP ID: rs1358782
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:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_006462.4:c.42-4192A>G
NM_031229.2:c.167+3309A>G
NT_011387.8:g.333978A>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 ss10955763 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1358782 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
ss2140986TSC-CSHL|TSC0498316fwd/BC/Tctacagattcaatgaaatccctaccaaaatcccagttgttgttgttttttttttgcagaa10/19/0010/10/0388Genomic95 %
ss8364368SC_SNP|NT_011387.8_333978rev/TA/Gttctgcaaaaaaaaaacaacaacaactgggattttggtagggatttcattgaatctgtag04/17/0310/10/03114Genomicunknown
ss10955763BCM_SSAHASNP|chr20.NT_011387.8_333978byFreqrev/TA/Gttctgcaaaaaaaaaacaacaacaactgggattttggtagggatttcattgaatctgtag06/30/0305/16/04116Genomicunknown
ss12483854WI_SSAHASNP|chr20.NT_011387.8_333978rev/TA/Gttctgcaaaaaaaaaacaacaacaactgggattttggtagggatttcattgaatctgtag07/04/0310/10/03116Genomicunknown
ss21779776SSAHASNP|WGSA-200403-chr20.chr20.NT_011387.8_333978rev/TA/Gttctgcaaaaaaaaaacaacaacaactgggattttggtagggatttcattgaatctgtag03/20/0403/20/04121Genomicunknown
ss41391768ABI|hCV1273466rev/TA/Gttctgcaaaaaaaaaacaacaacaactgggattttggtagggatttcattgaatctgtag07/17/0507/17/05126Genomicunknown
ss91612476BCMHGSC_JDW|JWB-1408819rev/TA/Gttctgcaaaaaaaaaacaacaacaactgggattttggtagggatttcattgaatctgtag02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1358782|allelePos=377|totalLen=3057|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 CTCTCAAAAC TCAGGTTCTG ACCCAGCAAG TCTGAGGTGA GACCTGAGAT TCCCCCCATG
 TTGTGGTCCA CAGGCCACAC TTTAGTAGCA AGATGGTGGC TGACATTGTA CATTTTACAA
 AGGAAACGCC AGTGCCAGTT AGTTAATTCA GGGGATCAAG TGGAAGTCAA CTGGGAAAGT
 GTCCACAATG ATACTTCaac aaaaaaagta aggaaaagga aaggtggaag atgagtatgt
 taacttcctc atttttcata gcaaggagta cacaggtact gtctcaaGCA atcatttcaa
 gaagtagata tctcaatatt ttgtttaaaa tcaagtggcc aatgatctac agattcaatg
 aaatccctac caaaat
 Y
 cccagttgtt gttgtttttt ttttgcagaa acagacaagc tgatcgtaaa atttatatgg
 aaattcaaga gacttgcaat aaccaaaaca atattgaaaa agaacaaaag ttggagaact
 tgtatttcct gatttcaaat actatgaagc tatagtaatt agtgtggtac tggcgtaagg
 gcagatatat attatagttc aatggtatag aaatgagagt ccagaaataa gcactcacat
 ttatggtcaa ttaatttcca aaaagggtta agatgattaa acagaggaaa acagccttaa
 caaatagtgc cggcacaact caatatccac gtgcaaaaga atgaagctgg acccttacct
 cacaccttat ataaaaatta aatcaaaatg gaccaaagac ctaaatgtaa gagctaaaac
 cataaaatct ttagaagaaa atatagaggt aaatcttcat gaccttggat gaggcaacga
 tttcttagat atgacaccaa aagcacaaac aacaaaataa aacatagact aactggacat
 catcaaaatt taaaactttt gtggttcaaa ggataccatc aacaaagtga gaagacaatc
 cacagaatga gagaaaattt ttgcaaatca tgtagctgat aagctaaaat gaataaagta
 cttctagcta aaatgaataa agtactccta caactcaata taaaaacata aacccagccg
 ggtgcagtgg ctcatgcctg taatcccaac actttggaaa ggccaaggtg ggtggatcac
 ctgaggtcag gagttcaaga ccagcctggc caacatggta agacccgtct ctactaaaaa
 tacaaaaatt agccagtgta gtggtgggca cctgtaatcc agctactcag gaggctgggg
 caggagaatc acttgaacct gggaggcgga ggttgcagtg agccgagatt gcaccattgc
 actcctgctt gggtgacaga gcgagactcc atctcaaaaa aaaaaaaaga taaacccaat
 tttaaaatgg gcaaaagacc tgaataggca aacctccaaa gaaaatatgt gcatgaaaag
 atgcttaaca tcatttgtca tcaaatggtt aggaaattgc aaatcaaaac cacagtgaga
 tacctcttca aacttactag gatggctata atcaaaaaga taaacaacaa caagtattag
 agatgatgtg gagaaactag aaccctcata tatgctggtg ggaatgtaaa atggtgcagc
 cactttggaa aactgtctgg catttcttca aaaagtaaca tagagttact gtatgaccca
 gcaattccac tgctagtgtg tatccaagag aaatgaaaac gtgtccacac aaaaagttgg
 acacaaatgt tcacggcagc attgtttata atagccaaaa aatagaaaca cccaaatgtc
 catcaactga tttaatgagt aaagataatg agatatgtct atacaataga ttattatttg
 gcaataaaaa ggaataaagt tctggttggg catggtggct cacacctgta atcccagcac
 tttgagaggc tgaggtggga agactgctta agccagaagt tcaagaccag cccagacaac
 aaagcaagac cttatctcta cagactttct aaaaattagc caggtgtggc tgggtgtggt
 ggctcacgcc tgtagtccca gcacattggg aggcataggc gggcggatca cgaggtcagg
 agatggagac catcctggtt aacacggcga aaccccgtct ctactaaaaa tacaaaaaat
 tagctgggcg tggtggcggg cgcctgtagt cccagctact cgggaagctg aggcaggaga
 atggcgtgaa cctgggaggt ggagcttgca gtgagctgag atcgcgccac tgcactccag
 cctgggggac agagtgagac tcccatctca aagaaaaaaa aaattagccg ggtgtggtgg
 tacatgccag tagtcccagc tacctgggag gccaaggcag gaggactgct tgaatccagg
 aagttgaggc tgtagtgagc gatgatggca ccactgcact tcaacctaga caagagaccc
 catgtcaaaa aaaaaaaggg gaatgaagtt gttagacatg ctacaacatg gatgaatctc
 gaaaacgatc ctaagtgaaa gaagccagat acaaaaggcc acatattgca tgattcaact
 tatatggaat ttccagaagg tagatcccta gagataaaaa gtagattagt ggttgcctaa
 ggttggggag ttagggaaaa ggtagagaga tgaggactgg ctgctaatga gtaccaggtt
 tctttacagg atgatgaaaa tgttctaaaa ttgattgtgg caatggttgc acaaccttga
 atatactaaa agccattgaa ctgtatactt taaatggtcg aactgtaagg ataaataaat
 aaataaaact gttttaagaa AAACCAAATG GGACCCACCA AGAGAACCAA AAATCAGAAA
 CCATAAAACT ATTGCCTTAC TATCCAGTAA TGAAAAAGCA GTCAAAAAAT AACGATAGAC
 ACTAATGTTT ATTATTGAGT GCATAACACG CCAGGCATTG TGCAAAGTGT TTCAGCATTG
 AGTTTAAGTC TCCTGGAGCA CAGACCGACA GTATCCATTC

  GeneView back to top
GeneView via analysis of contig annotation: RBCK1 RanBP-type and C3HC4-type zinc finger containing 1
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_011387->NM_006462
svfunction
referenceNT_011387->NM_031229
svfunction
HuRefNW_001838652->NM_006462
svfunction
HuRefNW_001838652->NM_031229
svfunction
CeleraNW_927317->NM_006462
svfunction
CeleraNW_927317->NM_031229
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011387->NM_006462->NP_006453333978forwardintron
referenceNT_011387->NM_031229->NP_112506333978forwardintron
HuRefNW_001838652->NM_006462->NP_006453345411forwardintron
HuRefNW_001838652->NM_031229->NP_112506345411forwardintron
CeleraNW_927317->NM_006462->NP_006453346002forwardintron
CeleraNW_927317->NM_031229->NP_112506346002forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1358782 maps exactly once on NCBI human chromosome 20
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
20NT_011387.8333978341978minusAref_assemblyreferencereferenceview376
20NW_001838652.1345411345411minusGalt_assembly_8HuRefHuRefview376
20NW_927317.1346002488826minusGalt_assembly_1CeleraCeleraview376

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011387
dbSNP Blast Analysis
GenBank HTGS Finished:
AL121747.41 NC_000020.9
UniGene Cluster ID
247280

  Population Diversity back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceHWPC
T
ss10955763CEPH 184AF 0.770 0.230

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.354+/-0.2270000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hit
DoubleHit found by:  BCM_SSAHASNP, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .