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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6121328          
refSNP ID: rs6121328
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:114/129
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_002110.2:c.62+3306C>T
NT_028392.5:g.839687C>T
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 ss10963981 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6121328 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
ss8449754SC_SNP|NT_028392.4_839687fwd/BC/Ttgtcagtagctcctaaacatttccatcaccctgaaaaaggaaactttgtacccattaagc04/17/0310/10/03114Genomicunknown
ss10963981BCM_SSAHASNP|chr20.NT_028392.4_839687byFreqfwd/BC/Ttgtcagtagctcctaaacatttccatcaccctgaaaaaggaaactttgtacccattaagc07/01/0310/25/06117Genomicunknown
ss23552771PERLEGEN|afd4575826byFreqfwd/BC/Ttgtcagtagctcctaaacatttccatcaccctgaaaaaggaaactttgtacccattaagc08/10/0409/13/04123Genomicunknown
ss67796229ILLUMINA|HumanHap650Yv1.0_rs6121328fwd/BC/Ttgtcagtagctcctaaacatttccatcaccctgaaaaaggaaactttgtacccattaagc11/14/0611/14/06127Genomicunknown
ss71446724ILLUMINA|HumanHap650Yv3.0_rs6121328fwd/BC/Ttgtcagtagctcctaaacatttccatcaccctgaaaaaggaaactttgtacccattaagc04/23/0704/23/07127Genomicunknown
ss75362759ILLUMINA|ILMN_Human_1M_rs6121328fwd/BC/Ttgtcagtagctcctaaacatttccatcaccctgaaaaaggaaactttgtacccattaagc08/28/0708/29/07129Genomicunknown
ss80923783HGSV|Cor18507_SNV_20070510.chr20_30107256fwd/BC/Ttgtcagtagctcctaaacatttccatcaccctgaaaaaggaaactttgtacccattaagc11/26/0711/27/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6121328|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTCAGGCCTC ATGTTCTCTG CTGTAAGGCA CTTCACTTGC CTTACTCACT ATGCCTGGCA
 CTTAATAAGT GTTCAAGAAA ATGGAAGCAT GAACCTTTTG AGGGAACAAT AACCAATATT
 TTCATGTATC TTTATGTAGT CTTTTCTATG CACTTTTAAA TTAACATAAT TAGTATAATG
 CTACACATAG ATTATTTTTA TCCTATTTAT TTGCTTAGTA TTACATTGTA GCATTTTCCA
 GGTCATTAAA ATGTTCTTAA ATTTTTAGTG GCTGCATAAT ATTCCACTGT TTGCCTGTAT
 TATAATTTGC TTAACCTTTC TAGCAGAGCA ATCTTTTATA TAGTTCAAAA TTTTTAGAAA
 TATTTTAATC GAGGTGAAAT TCACATAACT TTATAAAATT AACTATATGA TTTTTAAAGC
 GAACAATTCA GTGGTATTTG GTATATTCAC AATGTTGTAC AAACACTACC TGTCAGTAGC
 TCCTAAACAT TTCCATCACC
 Y
 CTGAAAAAGG AAACTTTGTA CCCATTAAGC AATTACCCCC CATTCCCCCG GCCCCTGGCA
 ACCACCAATC TGCTTTTTGC CTCTACGGAC TAATTTATTC AGGATATTTA ACATAAATAG
 AAGCATACTA TGTGACTTTC TGTGTCTAGC TTCTTCCACT TAACATAATG TTTTCCAAGG
 TTCATCCACA TGGTGGCAAC TATTAGTACT TTATTCCCTT TGTGGCCAAA TAATATTCCA
 TTGTATGGAT ATTCCACAGT TTATTTACCC ATTTATCCAC AGATGGAAAT TCAGGTTGTT
 TCCACATTTT GACCATTGAA AATAATACTG CTATGAGCAT GCATGTGCAT ACATGTATTT
 GTTTGAGCAC CTGTTTTCAA TTCCTTTGGG TATATACCTG AAGTAGAGTT ACTGGGTCAT
 ATAAAAGTTC TATCTCTGTG GCCGGGTGCG GTGGCTCACG CCTGTAATCC CAGCACTCTG
 GGAGGCTGAG GCGGGCGGAT

  GeneView back to top
GeneView via analysis of contig annotation: HCK hemopoietic cell kinase
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_028392->NM_002110
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_028392->NM_002110->NP_002101839687forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6121328 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
20NW_927339.190306227399953plusCalt_assembly_1CeleraCeleraview500
20NW_001838664.2424773327432257minusGalt_assembly_8HuRefHuRefview500
20NT_028392.583968730107256plusCref_assemblyreferencereferenceview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_028392
dbSNP Blast Analysis
GenBank HTGS Finished:
AL353092.6

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss10963981HapMap-CEUEuropean 94IG 0.957 0.043 1.000 0.979 0.021
HapMap-HCBAsian 74IG 0.919 0.081 1.000 0.959 0.041
HapMap-JPTAsian 80IG 0.925 0.075 0.963 0.037
HapMap-YRISub-Saharan African 106IG 0.717 0.264 0.019 1.000 0.849 0.151
ss23552771AFD_EUR_PANELEuropean 44IG 0.955 0.045 1.000 0.977 0.023
AFD_AFR_PANELAfrican American 44IG 0.682 0.318 0.403 0.841 0.159
AFD_CHN_PANELAsian 46IG 0.957 0.043 1.000 0.978 0.022

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.126+/-0.21733226090

  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 .