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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs733023          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
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_015082.1:c.410-3281G>T
NT_034772.5:g.35070638A>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 ss44677235 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs733023 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
ss78754TSC-CSHL|TSC0022796byFreqfwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga09/06/0010/25/0686Genomic95 %
ss5459286TSC-CSHL|TSC0161146rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct09/21/0210/25/06108Genomicunknown
ss5969445SC_JCM|NT_034775.1_210587rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct01/10/0310/10/03111Genomicunknown
ss17062629CSHL-HAPMAP|CSHL-HuAA-200402.chr5.NT_034772.5_35070638rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct02/17/0403/04/04120Genomicunknown
ss19621001CSHL-HAPMAP|CSHL-HuDD-200402.chr5.NT_034772.5_35070638rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct02/20/0403/04/04120Genomicunknown
ss22308237SSAHASNP|WGSA-200403-chr5.chr5.NT_034772.5_35070638rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct03/21/0403/21/04121Genomicunknown
ss23950700PERLEGEN|afd2506513byFreqrev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct08/10/0409/13/04123Genomicunknown
ss44677235ABI|hCV2930811byFreqrev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct07/19/0511/03/06126Genomicunknown
ss65830658KRIBB_YJKIM|KHS6450byFreqfwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga10/17/0612/16/06127Genomicunknown
ss66565253ILLUMINA|HumanHap300v1.1_rs733023fwd/TC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga11/09/0611/09/06127Genomicunknown
ss67570627ILLUMINA|HumanHap550v1.1_rs733023fwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga11/14/0611/14/06127Genomicunknown
ss67950854ILLUMINA|HumanHap650Yv1.0_rs733023fwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga11/14/0611/15/06127Genomicunknown
ss70923870ILLUMINA|HumanHap550v3.0__rs733023fwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga04/20/0703/31/08130Genomicunknown
ss71524389ILLUMINA|HumanHap650Yv3.0_rs733023fwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga04/23/0704/23/07127Genomicunknown
ss75618776ILLUMINA|ILMN_Human_1M_rs733023fwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga08/28/0708/29/07129Genomicunknown
ss78542400HGSV|Cor12878_SNV_20070510.chr5_132683524rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct10/17/0710/19/07129Genomicunknown
ss79254505ILLUMINA|HumanHap300v2.0_rs733023fwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga04/18/0711/18/07130Genomicunknown
ss83539117KRIBB_YJKIM|KHS485153fwd/BC/Tagcatcaggctgcctttcctccagggtccaggcccttccccagtgctgtcgggcaccaga12/04/0712/05/07130Genomicunknown
ss98649602HUMANGENOME_JCVI|1103654227427rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct04/01/0804/01/08130Genomicunknown
ss1094294901000GENOMES|CEU.trio.12.15.2008_1366517_chr5_132683524rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct12/15/0812/16/08130Genomicunknown
ss1132915401000GENOMES|NA19240_2008_12_16_1227978_chr5_132683524rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct12/18/0812/18/08130Genomicunknown
ss116819285ILLUMINA-UK|NA18507_000168446_NCBI36.1_chr5_132683524rev/TA/Gtctggtgcccgacagcactggggaagggcctggaccctggaggaaaggcagcctgatgct01/17/0901/18/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs733023|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTGTGAGGGA GGAAATCTAT CCAGGGAGAC TGAGCTGGAG GCTGCAGCTT TGGGGCATCT
 GCCTCTGGGG GCTGGAAGAA GGCAAGGAAG GAAGTTTTCC CTCCCCCACT CCACCTCAAG
 CCCTGTGGAA TTCGGATGAC AAAGGCAGGG AGTGAAGGCA GGGAGCCACC AAGAGGGCAG
 CCCTTGGAGA TGAAGGCTCA AAAGCCTTCC CAAAAAGCGA GTTTGGACTT TGGGATCTCG
 AGTGATCATC TGCACAGAAG CAGAGCTCTG AGCATCAGGC TGCCTTTCCT CCAGGGTCCA
 Y
 GGCCCTTCCC CAGTGCTGTC GGGCACCAGA GGAGCTCAGT AATTTCGGAC AAATGACTTC
 ATGATTTAAG TTTGGGCAAA GTTCTCTCTT GCAACTCATT AAAGCACAGT TGCTCCTGGG
 GTAAAGAAGG ATTTAAGATT CTGTTCCTGG AATCCCTTGG TTCATCTCAG GACCCCAGTG
 GCAAGCTTGG CCCGGGCATG GAGTGCCCTC AGTAAAGGGA AGAAATGACG AAGGAAGTTT
 TGAACAGCAT GATGTACGGT GCCACACACT TCCCCAAGGC CTTGGAGGCT CTGCCTGGGT

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_034775.1 ABBA01068778
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss23950700 AFD_EUR_PANEL European 48 IG 0.625 0.375 0.273 0.812 0.188
AFD_AFR_PANEL African American 46 IG 0.565 0.391 0.043 0.752 0.761 0.239
AFD_CHN_PANEL Asian 48 IG 0.417 0.417 0.167 0.655 0.625 0.375
ss44677235 HapMap-CEU European 120 IG 0.400 0.517 0.083 0.251 0.658 0.342
HapMap-HCB Asian 90 IG 0.267 0.578 0.156 0.254 0.556 0.444
HapMap-JPT Asian 90 IG 0.311 0.489 0.200 1.000 0.556 0.444
HapMap-YRI Sub-Saharan African 120 IG 0.483 0.400 0.117 0.584 0.683 0.317
ss65830658 KHP1 170 AF 0.294 0.412 0.294 0.150 0.500 0.500
ss78754 TSC_42_AA 80 AF 0.625 0.375
TSC_42_C 84 AF 0.631 0.369
TSC_42_A 82 AF 0.476 0.524

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.474+/-0.112 1264 1052 15 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .