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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs895497          
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_014440.1:c.35A>G
NP_055255.1:p.Gln12Arg
NT_022135.15:g.2471498A>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 ss1325858 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs895497 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
ss1325858TSC-CSHL|TSC0168638byFreqfwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg09/06/0004/07/0486Genomic95 %
ss9909995BCM_SSAHASNP|chr2.NT_022135.13_2471318rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt06/27/0310/10/03116Genomicunknown
ss11435187WI_SSAHASNP|chr2.NT_022135.13_2471318rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt07/03/0310/10/03116Genomicunknown
ss16812343CSHL-HAPMAP|CSHL-HuAA-200402.chr2.NT_022135.13_2471318rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt02/17/0403/04/04120Genomicunknown
ss19411522CSHL-HAPMAP|CSHL-HuDD-200402.chr2.NT_022135.13_2471318rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt02/20/0403/04/04120Genomicunknown
ss21570433SSAHASNP|WGSA-200403-chr2.chr2.NT_022135.13_2471318rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt03/20/0403/20/04121Genomicunknown
ss37042400PGA-UW-FHCRC|IL1F6-010131byFreqrev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt04/07/0511/02/06125Genomicunknown
ss44211375ABI|hCV2146491rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt07/18/0507/18/05126Genomicunknown
ss66629276ILLUMINA|HumanHap300v1.1_rs895497fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg11/09/0611/09/06127Genomicunknown
ss67889790ILLUMINA|HumanHap550v1.1_rs895497fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg11/14/0611/14/06127Genomicunknown
ss68026890ILLUMINA|HumanHap650Yv1.0_rs895497fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg11/14/0611/15/06127Genomicunknown
ss68824674PERLEGEN|PGP04749778byFreqrev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt01/30/0708/14/07127Genomicunknown
ss71591533ILLUMINA|HumanHap650Yv3.0_rs895497fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg04/23/0704/23/07127Genomicunknown
ss74809979AFFY|SNP_M-183051fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg08/09/0708/09/07128Genomicunknown
ss75453659ILLUMINA|ILMN_Human_1M_rs895497fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg08/28/0708/29/07129Genomicunknown
ss77798200HGSV|Cor12156_SNV_20070510.chr2_113479806rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt10/09/0710/14/07129Genomicunknown
ss78768957HGSV|Cor12878_SNV_20070510.chr2_113479806rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt10/17/0710/20/07129Genomicunknown
ss79287536ILLUMINA|HumanHap300v2.0_rs895497fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg04/18/0711/18/07130Genomicunknown
ss81007411HGSV|Cor18507_SNV_20070510.chr2_113479806rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt11/26/0711/27/07130Genomicunknown
ss83599515KRIBB_YJKIM|KHS498913fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg12/04/0712/05/07130Genomicunknown
ss85147284HGSV|Cor19240_SNV_20070510.chr2_113479806rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt11/30/0712/08/07130Genomicunknown
ss91298924BCMHGSC_JDW|JWB-1289298rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt02/26/0803/01/08129Genomicunknown
ss97066599HUMANGENOME_JCVI|1103658186999rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt03/28/0803/28/08130Genomicunknown
ss98231232ILLUMINA|HumanHap550v3.0__rs895497fwd/BC/Tacccgatgattgatatcctgaatgctccccgctgaggtgtgtcaattttcaatgctgttg04/20/0703/31/08130Genomicunknown
ss106110818BGI|BGI_rs895497rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt09/13/0806/18/09130Genomicunknown
ss1097868571000GENOMES|CEU.trio.12.15.2008_445472_chr2_113480046rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt12/15/0812/16/08130Genomicunknown
ss1107517101000GENOMES|NA19240_2008_12_16_405193_chr2_113480046rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt12/16/0812/17/08130Genomicunknown
ss117831262ILLUMINA-UK|NA18507_000141475_NCBI36.1_chr2_113480046rev/TA/Gcaacagcattgaaaattgacacacctcagcggggagcattcaggatatcaatcatcgggt01/19/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs895497|allelePos=569|totalLen=640|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTGCCATTTC CAGGGTGGTA CCTCTGAGCC AGAGTTTTAA GGGAATCTGC TAACTGACAC
 TCACAGTGCA CTCATAGAAT GGTCACCTCA CCACCCACCA CCTAACCGGG ACACCCATCC
 TATGTTTGGG GAACACTTTC CATTAGAAAA GTCAGTCTTT CATGGATTCA AAAACTGGTC
 CTCCCATAGA TTACCCTCTT TTGTCCTACT CTTACTCCTT GAAGTTTCTC AGAATACGTC
 TTCCACTGTT TTTCATAGGC TGACCCTTCA GTCTCCCTTA AGCCTTCTCT CTCTTCTCTG
 ACTTCATGAC CATAGTCCCA GAACAACCTT ATGCTCACCC TCTATTCATT ATTGTCTGTG
 AGATGCTCCT CTCTGTAGAT ATGCCCGGTT AACAAGCCCA CTGTGGAATA ACATCTGAGC
 ACCAAACACA CAACAGCACT GGCCAAAGGA GCTGCCTTTC ACAGACCGTG GCTACTCACC
 TGGAGACATA CGGTCCTTCC TCGGGACTGC TATGAGCGTC TGGTCCTGAA GAACCCACAC
 CCGATGATTG ATATCCTGAA TGCTCCCC
 Y
 GCTGAGGTGT GTCAATTTTC AATGCTGTTG AGAAAGTCAA AATGTAAATT AGTAAGAATG
 AGAGCACAGA A

  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_022135 ABBA01074248
dbSNP Blast Analysis
UniGene Cluster ID
278910

  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
ss1325858 CEPH 184 AF 0.680 0.320
HapMap-CEU European 120 IG 0.483 0.367 0.150 0.200 0.667 0.333
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.533 0.417 0.050 0.527 0.742 0.258
ss37042400 PGA_CEPH-PANEL European 46 IG 0.609 0.217 0.174 0.050 0.717 0.283
PGA_YORUB-PANEL Sub-Saharan African 46 IG 0.478 0.522 0.100 0.739 0.261
ss68824674 HapMap-CEU European 120 GF 0.483 0.367 0.150 0.667 0.333
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.533 0.417 0.050 0.742 0.258

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.295+/-0.246 1208 1002 270 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: ILLUMINA
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN YES

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Revised: May 25, 2006 1:38 PM .