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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1221362          
refSNP ID: rs1221362
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/129
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
NT_011651.16:g.22292966T>C
XM_001726957.1:c.40+14667A>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 ss8506848 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1221362 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
ss1787725KWOK|OVLP-000925-464613byFreqfwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca10/05/0004/07/0487Genomic99 %
ss2593560SC_JCM|AL137843.4_14291fwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca11/03/0010/10/0389Genomicunknown
ss8506848SC_SNP|NT_011651.13_22237224byFreqrev/BC/Ttgtttttcttgcttttgggtccctgactagattgacttttaacctcatctcaaactctat05/23/0304/07/04116Genomicunknown
ss23829331PERLEGEN|afd3847129byFreqrev/BC/Ttgtttttcttgcttttgggtccctgactagattgacttttaacctcatctcaaactctat08/10/0409/13/04123Genomicunknown
ss66669461ILLUMINA|HumanHap300v1.1_rs1221362fwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca11/09/0611/09/06127Genomicunknown
ss66991087ILLUMINA|HumanHap550v1.1_rs1221362fwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca11/14/0611/14/06127Genomicunknown
ss67166080ILLUMINA|HumanHap650Yv1.0_rs1221362fwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca11/14/0611/14/06127Genomicunknown
ss69263996PERLEGEN|PGP03847129byFreqrev/BC/Ttgtttttcttgcttttgggtccctgactagattgacttttaacctcatctcaaactctat01/30/0708/14/07127Genomicunknown
ss70406757ILLUMINA|HumanHap300v2.0_rs1221362fwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca04/18/0711/18/07127Genomicunknown
ss70560141ILLUMINA|HumanHap550v3.0__rs1221362rev/BC/Ttgtttttcttgcttttgggtccctgactagattgacttttaacctcatctcaaactctat04/20/0703/30/08130Genomicunknown
ss71098094ILLUMINA|HumanHap650Yv3.0_rs1221362fwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca04/23/0704/23/07127Genomicunknown
ss75577530ILLUMINA|ILMN_Human_1M_rs1221362fwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca08/28/0708/29/07129Genomicunknown
ss79725830HGSV|Cor18507_SNV_20070510.chrX_98802803rev/BC/Ttgtttttcttgcttttgggtccctgactagattgacttttaacctcatctcaaactctat11/23/0711/23/07130Genomicunknown
ss83702559KRIBB_YJKIM|KHS523158fwd/TA/Gatagagtttgagatgaggttaaaagtcaatctagtcagggacccaaaagcaagaaaaaca12/04/0712/05/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1221362|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 ACTTATAGCT AATATTATTC TCATTTTTTT TCAGCCTGGG TAAGATAGAC ATGATACATC
 TATCAATAAA GAAACTCAAA GAAGATATGG AAGCAATGGA TATTAGTCCT TTATACCAAG
 AGTTGCAATC TTTCCTTTTA ATCAGGAAGA CTCCGACTTC ATAGATCAGA CCCAATTCTT
 CAGCTTTTCT CATCCACACT GTGTTGGAAT CTGTATTGTA TCTTATCCAG GTAAGTTCAT
 GTCACACTGG CCTTCAGGCA TTAGTGTATC CCAGAAATAG GAATATAAAC CAGAAGTGAA
 GAGGCATAAC AGAGTCTAGA GCCAGAACAA AGAGATGTTG ACAGTATTGG AACATAAGAA
 AAATAAAATA ATAGAGTTTG AGATGAGGTT AAAAGTCAAT
 R
 CTAGTCAGGG ACCCAAAAGC AAGAAAAACA AGCCAGATAT TATATTCAAG AAATAGCTTA
 AAACACTGTA AATAATCTGT GGAACATTCA TAAAGTACCA AAAATAGAAA TTGATATAAA
 ATTTGCCTCT AAAGTAAGTT TTACTATAGC CTATAACAAC GACCAGTTTA CCTATGGTGA
 ACAAGGCCAA AAAGGCTTAA CTGTGCAGTG ACTTGTCACA CGTGAAAGAG ATTTGGTTTG
 TTTCACAAAT ACATAAGTCC ATTGTGTTAT TCATTTACCC TCCTGACATT CACCTTAAAT
 CCAGGCCTTC ATAGATTCAT TGGTCTATGT ATACTTTCTT TTGGTTTCTA AGATGAAGAA
 TAAATGTGGC TGAAAATCAG AGCTAGTTAC TCCCTCCCCT

  GeneView back to top
GeneView via analysis of contig annotation: LOC442459 X-ray repair complementing defective repair pseudogene
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_011651->XM_001726957
function
HuRefNW_001842386->XM_001716243
function
CeleraNW_927715->XM_001726964
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011651->XM_001726957->XP_00172700922292966reverseintron
HuRefNW_001842386->XM_001716243->XP_0017162951239610forwardintron
CeleraNW_927715->XM_001726964->XP_00172701610678946reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1221362 maps exactly once on NCBI human chromosome X
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
XNW_001842386.2123961088799152plusAalt_assembly_8HuRefHuRefview400
XNT_011651.162229296698883314minusTref_assemblyreferencereferenceview400
XNW_927715.11067894699517163minusTalt_assembly_1CeleraCeleraview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011651 AL358953 AL358953.4
dbSNP Blast Analysis
GenBank HTGS Finished:
AL137843.4

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss1787725TSC_42_AA 84AF 0.300 0.700
TSC_42_C 84AF 1.000
TSC_42_A 84AF 0.850 0.150
ss23829331AFD_EUR_PANELEuropean 48IG 0.750 0.167 0.083 0.100 0.833 0.167
AFD_AFR_PANELAfrican American 46IG 0.174 0.261 0.565 0.100 0.304 0.696
AFD_CHN_PANELAsian 48IG 0.583 0.292 0.125 0.200 0.729 0.271
ss69263996HapMap-CEUEuropean 60GF 0.383 0.117 0.589 0.078
HapMap-HCBAsian 46GF 0.200 0.244 0.067 0.426 0.250
HapMap-JPTAsian 44GF 0.244 0.156 0.089 0.433 0.224
HapMap-YRISub-Saharan African 60GF 0.033 0.233 0.233 0.200 0.467
ss8506848HapMap-CEUEuropean 120IG 0.850 0.117 0.033 0.752 0.908 0.092
HapMap-HCBAsian 90IG 0.467 0.244 0.289 1.000 0.589 0.411
HapMap-JPTAsian 88IG 0.591 0.159 0.250 0.200 0.670 0.330
HapMap-YRISub-Saharan African 120IG 0.200 0.233 0.567 0.584 0.317 0.683

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.471+/-0.1163322602700

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: ILLUMINA, PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .