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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs248221          
refSNP ID: rs248221
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_018434.4:c.945+908A>G
NT_023133.12:g.24206088T>C
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 ss1780587 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs248221 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
ss320415KWOK|OVLP-000621-20948rev/TA/Gagagagaaggacatgatttttcttcattccgtacctacctttagaaggtaggctgtatgc06/30/0010/10/0379Genomic99 %
ss628792SC_JCM|AC010285.4_86229fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct07/12/0010/10/0387Genomicunknown
ss1165683KWOK|OVLP-000804-521486fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct09/02/0010/10/0386Genomic99 %
ss1250895KWOK|OVLP-000804-528740fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct09/02/0010/10/0386Genomic97 %
ss1780587KWOK|OVLP-000925-361494byFreqfwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct10/05/0010/21/0489Genomic99 %
ss1829114KWOK|OVLP-000925-368513fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct10/05/0010/10/0389Genomic97 %
ss2472594SC_JCM|AC010313.5_15736fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct11/03/0010/10/0392Genomicunknown
ss4984148YUSUKE|IMS-JST155862rev/TA/Gagagagaaggacatgatttttcttcattccgtacctacctttagaaggtaggctgtatgc08/12/0210/10/03108Genomicunknown
ss6475077WI_SSAHASNP|NT_006519.11_1248983fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct02/12/0310/10/03111Genomicunknown
ss11724959WI_SSAHASNP|chr5.NT_077451.2_2487769fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct07/03/0310/10/03116Genomicunknown
ss44642397ABI|hCV2929455fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct07/19/0507/19/05126Genomicunknown
ss66807552ILLUMINA|HumanHap300v1.1_rs248221fwd/TC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct11/09/0611/09/06127Genomicunknown
ss67256936ILLUMINA|HumanHap550v1.1_rs248221fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct11/14/0611/14/06127Genomicunknown
ss67655435ILLUMINA|HumanHap650Yv1.0_rs248221fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct11/14/0611/14/06127Genomicunknown
ss70735292ILLUMINA|HumanHap550v3.0__rs248221fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct04/20/0703/30/08130Genomicunknown
ss71305360ILLUMINA|HumanHap650Yv3.0_rs248221fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct04/23/0704/23/07127Genomicunknown
ss75821251ILLUMINA|ILMN_Human_1M_rs248221fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct08/28/0708/29/07129Genomicunknown
ss79136730ILLUMINA|HumanHap300v2.0_rs248221fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct04/18/0711/18/07130Genomicunknown
ss83401516KRIBB_YJKIM|KHS452925fwd/BC/Tgcatacagcctaccttctaaaggtaggtacggaatgaagaaaaatcatgtccttctctct12/04/0712/04/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs248221|allelePos=201|totalLen=994|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TGTGGTTGTC AACAGTTCTC CTGGGCTCCA GGTCACTGCC TGCCTTCTCT GCTTGCAACT
 TACCAACCCT CAAGAGATCA AAGTCAAACT TCAGGCTAAA GAACATAAGC AAGACATCGT
 TTTATATTAT GCCAAGCACA GAGGAGTTTA TGACTGGAAC AGAGTCAACA GCATACAGCC
 TACCTTCTAA AGGTAGGTAC
 Y
 GGAATGAAGA AAAATCATGT CCTTCTCTCT TTCTTCATCC CATACTCATC GACCAACAGA
 AGCACCCTTT TAAAAGTGGA CCATgccagg tgtggtgact cacgcctata atcccagcac
 tttgggaggc tgaggcagga ggatcacttg aggccaggag ttgagacccg cctgaacatc
 ttgtctcttc aaaacataaa aaagtggcca ggcacggtgg ctcacgcctg taaccccagc
 actttgggag gcagaggcgg gtggatcacc tgaggtcagg agttggagac cagcctggac
 aacatggtga aaccctgtct ctactaaaaa tacaaaaaat tagccagggg tggtgacggg
 cacctgcaat cccagctact cagaaggctg aggcaggaga atcgcttgaa cctgggaggc
 ggaggttgca gtgagccaag atcgtgccat tgtactccag cttgggcaac aagagcaaaa
 ctccctctca aaaaaacaaa aaagttagcc aggcatggcg gtgtatgcct gtagtcccag
 ctactcagaa ggcgaggtgg gaggactgct tgaacccagg agttcgaggt tacagtaagc
 tatgattgca ccactacact ccagcttggg ccacagagtg aatccttgtc tcttaaattt
 aaaaaaagaa aaaaaaaGGC CTAGTAGAGT TATTTACCTT CTCTTCCAGG AGTTCTCTGA
 GATGGATTAG ACTTCTTAGT AATCTGGTAA AAAGGTCCTG TTGGGCTTAC ATGGTTACAT
 GGCAAATATA GCC

  GeneView back to top
GeneView via analysis of contig annotation: RNF130 ring finger protein 130
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_023133->NM_018434
svfunction
HuRefNW_001838967->NM_018434
svfunction
CeleraNW_922818->NM_018434
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_023133->NM_018434->NP_06090424206088reverseintron
HuRefNW_001838967->NM_018434->NP_0609041925590reverseintron
CeleraNW_922818->NM_018434->NP_0609041919041reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs248221 maps exactly once on NCBI human chromosome 5
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
5NW_001838967.11925590174121258plusTalt_assembly_8HuRefHuRefview200
5NW_922818.11919041175021693plusTalt_assembly_1CeleraCeleraview200
5NT_023133.1224206088179329108plusTref_assemblyreferencereferenceview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_077451 AC010313 AC010313.5 AC026413 AC026413.3
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC010285.4 AC026413.5 NC_000005.8 AC010313.5

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1780587HapMap-CEUEuropean 120IG 0.050 0.367 0.583 1.000 0.233 0.767
HapMap-HCBAsian 90IG 0.244 0.756 0.403 0.122 0.878
HapMap-JPTAsian 90IG 0.022 0.156 0.822 0.403 0.100 0.900
HapMap-YRISub-Saharan African 120IG 0.183 0.817 0.479 0.092 0.908

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.241+/-0.25027021000

  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 .