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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2305089          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
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_003181.2:c.530G>A
NP_003172.1:p.Gly177Asp
NT_007422.13:g.8866611C>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 ss44710082 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2305089 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
ss3252182YUSUKE|IMS-JST062267byFreqfwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct09/05/0110/10/03100Genomicunknown
ss11794004WI_SSAHASNP|chr6.NT_007422.12_8866611fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct07/04/0310/10/03116Genomicunknown
ss13080656SC_SNP|NT_007422.12_8866611fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct10/22/0310/31/03119Genomicunknown
ss17132351CSHL-HAPMAP|CSHL-HuAA-200402.chr6.NT_007422.12_8866611fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct02/17/0403/04/04120Genomicunknown
ss44710082ABI|hCV11223433byFreqfwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct07/19/0511/03/06126Genomicunknown
ss48426970APPLERA_GI|hCV11223433byFreqrev/TA/Gagcctcgaatccacatagtgagagttggggtccacagcgcatgatcaccagccactgctt09/28/0511/03/06126Genomicunknown
ss66581424ILLUMINA|HumanHap300v1.1_rs2305089fwd/TC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct11/09/0611/09/06127Genomicunknown
ss67245268ILLUMINA|HumanHap550v1.1_rs2305089fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct11/14/0611/14/06127Genomicunknown
ss67642289ILLUMINA|HumanHap650Yv1.0_rs2305089fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct11/14/0611/14/06127Genomicunknown
ss69000606PERLEGEN|PGP04554353byFreqfwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct01/30/0708/14/07127Genomicunknown
ss70723602ILLUMINA|HumanHap550v3.0__rs2305089rev/TA/Gagcctcgaatccacatagtgagagttggggtccacagcgcatgatcaccagccactgctt04/20/0703/30/08130Genomicunknown
ss71292203ILLUMINA|HumanHap650Yv3.0_rs2305089fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct04/23/0704/23/07127Genomicunknown
ss74807558AFFY|SNP_M-178756fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct08/09/0708/09/07128Genomicunknown
ss74957072ILLUMINA|ILMN_Human_1M_rs2305089fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct08/28/0708/29/07129Genomicunknown
ss78440398HGSV|Cor12878_SNV_20070510.chr6_166549681fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct10/17/0710/19/07129Genomicunknown
ss79128857ILLUMINA|HumanHap300v2.0_rs2305089fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct04/18/0711/18/07130Genomicunknown
ss84030830KRIBB_YJKIM|KHS607278fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct12/04/0712/06/07130Genomicunknown
ss1113082401000GENOMES|CEU.trio.12.15.2008_1674073_chr6_166499260fwd/BC/Taagcagtggctggtgatcatgcgctgtggaccccaactctcactatgtggattcgaggct12/15/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2305089|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 AAACACTTGT ATGGAGAATT CAAGGGGAAA ATGTTTGAAT GGGGACTTAA TTTAAACAGT
 TCTCTCCTGT GCTTCCATTT CAAGTTCCGG AATATTATTT GAAAGGGCAG GAAGCCTTCC
 TCTCAGTGCG GGTTAGCGCG TCTCCCCGCT CCTCCAGAAT CTCCACGGAG CAGCACACCA
 CACCGCAGCA CACCGGGAAA GCGATCCGCC TCTGTCCTTC TCACCTCCTC GTTCTGATAA
 GCAGTCACCG CTATGAACTG GGTCTCAGGG AAGCAGTGGC TGGTGATCAT GCGCTGTGGA
 Y
 CCCCAACTCT CACTATGTGG ATTCGAGGCT CATACTTATG CAAGGAGTTC AGCATGATCT
 GAGGGAGACA GATACAGGAT TGGTGGCACT GAAAGGCCTG CGTTAAAACA GCAAAACATC
 CATTTCTCCA GGATGCAGAA AGTCCTCTGG ATCCCAAGAA AGTGTCTCTG CTGTTGAGGG
 AAGTGGGGTT CCACCAGGGG AGGCTTCTCC GCGGTTTATA TGTGCTATTC CCACAGCTTG
 TTTGGAAAAG GGATGTGAGA TGCTACACAC CATTAAAAGC AATGAATGCT CATCACAAAA

  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_007422
dbSNP Blast Analysis
UniGene Cluster ID
389457

  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
ss3252182 JBIC-allele 1498 AF 0.666 0.334
ss44710082 HapMap-CEU European 120 IG 0.200 0.417 0.383 0.294 0.408 0.592
HapMap-HCB Asian 90 IG 0.422 0.444 0.133 1.000 0.644 0.356
HapMap-JPT Asian 88 IG 0.523 0.364 0.114 0.403 0.705 0.295
HapMap-YRI Sub-Saharan African 120 IG 0.633 0.300 0.067 0.371 0.783 0.217
AoD_African_American 90 AF 0.710 0.290
ss48426970 AGI_ASP population multiple 78 IG 0.282 0.615 0.103 0.100 0.590 0.410
ss69000606 HapMap-CEU European 120 GF 0.200 0.450 0.350 0.425 0.575
HapMap-HCB Asian 90 GF 0.422 0.467 0.111 0.656 0.344
HapMap-JPT Asian 90 GF 0.533 0.356 0.111 0.711 0.289
HapMap-YRI Sub-Saharan African 120 GF 0.633 0.300 0.067 0.783 0.217
Concordant Genotype Total Sample C/C C/T T/T
ss44710082 1204 476 500 188
ss48426970 39
ss69000606 267 118 100 49
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs2305089 1246 494 509 191
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
169 ss44710082 T/T CSHL-HAPMAP HapMap-CEU NA06994 CEPH1340.09 r27_ch6_CEU_illumina:human_1m_beadchip 510337
169 ss69000606 C/T CSHL-HAPMAP HapMap-CEU NA06994 CEPH1340.09 chr6-HapMap-CEU
185 ss44710082 T/T CSHL-HAPMAP HapMap-CEU NA07055 CEPH1341.12 r27_ch6_CEU_illumina:human_1m_beadchip 510337
185 ss69000606 C/T CSHL-HAPMAP HapMap-CEU NA07055 CEPH1341.12 chr6-HapMap-CEU
5173 ss44710082 T/T CSHL-HAPMAP HapMap-HCB NA18612 CH18612 r27_ch6_CHB_illumina:human_1m_beadchip 510337
5173 ss69000606 C/T CSHL-HAPMAP HapMap-HCB NA18612 CH18612 chr6-HapMap-HCB
Genotype data submitted for1246 samples from1246 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .