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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2013526          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:92/130
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_199351.1:c.881-3390T>A
NT_004487.18:g.17390162T>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 ss90742 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2013526 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
ss90742TSC-CSHL|TSC0110134byFreqfwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca09/06/0010/25/06108Genomicunknown
ss2890249TSC-CSHL|TSC0013419byFreqfwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca01/03/0110/25/0692Genomicunknown
ss9854975BCM_SSAHASNP|chr1.NT_004668.15_13270366fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca06/27/0310/10/03116Genomicunknown
ss16398873CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_004668.16_5405279fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca02/17/0403/04/04120Genomicunknown
ss20567658SSAHASNP|WGSA-200403-chr1.chr1.NT_004668.16_5405279fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca03/18/0403/18/04121Genomicunknown
ss44079070ABI|hCV8918028fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca07/18/0507/18/05126Genomicunknown
ss46535560PERLEGEN|PS00691857fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca08/01/0508/01/05126Genomicunknown
ss67215351ILLUMINA|HumanHap550v1.1_rs2013526fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca11/14/0611/14/06127Genomicunknown
ss67609030ILLUMINA|HumanHap650Yv1.0_rs2013526fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca11/14/0611/14/06127Genomicunknown
ss68193870ILLUMINA|HumanHap250Sv1.0_rs2013526fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca12/06/0612/07/06127Genomicunknown
ss70693614ILLUMINA|HumanHap550v3.0__rs2013526rev/TA/Gtgacatagagccagattctaccaggatcaggaatagtttagtatatttgaacttgtagct04/20/0703/30/08130Genomicunknown
ss71258903ILLUMINA|HumanHap650Yv3.0_rs2013526fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca04/23/0704/23/07127Genomicunknown
ss75744296ILLUMINA|ILMN_Human_1M_rs2013526fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca08/28/0708/29/07129Genomicunknown
ss83944291KRIBB_YJKIM|KHS579959fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca12/04/0712/06/07130Genomicunknown
ss87856796BCMHGSC_JDW|JWB-0140466fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca02/26/0802/26/08129Genomicunknown
ss1086708711000GENOMES|CEU.trio.12.15.2008_179743_chr1_165166431fwd/BC/Tagctacaagttcaaatatactaaactattcctgatcctggtagaatctggctctatgtca12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2013526|allelePos=432|totalLen=796|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTGGGAGATC CTCAGTTAAT TGCCACTTGG ACTAGAGCAT AGTTTTCTAT GTCATTATAA
 CAAATTACAC TCCTCATTAT GATACAGATT TGATTGTGTA TGCATAGGTT ATCATGTCCC
 CTGAAAAGTT ACAGTAACCA TTTATAGCCT CAAATGAAGA TGATAGTTTT GCCTTCAGTG
 CTGGCATTAT AAAGAGACTC CACTGTACCA GATACTTTCA GCCTTGACTT CTTAGTCACA
 GCAGCCCATG ACTTCAGAAA TCTAAATTCC TCTAATTTGT CAAAAAAGAC AGAGGCAAAG
 TATTGATCTT TTGACTTTAG GAGTATCATC CATTTGGTTT CAGTAGCTAA AAACCTGGGC
 AATTCTCCTT CTAAAAGCTA TTGGACTTTT TAAAAATGAT AAGCTACAAG TTCAAATATA
 CTAAACTATT C
 Y
 CTGATCCTGG TAGAATCTGG CTCTATGTCA CATACATTCT GAGGAGCATA TGAAACACCA
 GAAAACCTTT CCTGGTCCCT CCTCTCCAAG GATGAGATTT TCCTTTCTGA GCTGGCATTA
 TGGATCAATC TTATACTGCC TTGTATTACT TACTCATTTT ATTTCCACTT ACAAGCCCCA
 GCAACCACCT GGTAGACTGT ACATTCCTTG ACGGCAGGTA AAATTTGTTA GCGTTCATTA
 AATTTTTCTT GATTTGACAG CAAATAGCAT GGTGTCAGAT TGATTTTTAT CTGTGATTTG
 TCTGAAGAAC ACAAACTCTC TGGACTATGG TGATGTTTTA ATAAAAATGT CCTAAACTAT
 TGGC

  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_004668
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
ss2890249 TSC_42_AA 82 AF 0.488 0.512
TSC_42_C 84 AF 0.512 0.488
TSC_42_A 82 AF 0.622 0.378
ss90742 HapMap-CEU European 120 IG 0.083 0.600 0.317 0.050 0.383 0.617
HapMap-HCB Asian 90 IG 0.378 0.489 0.133 1.000 0.622 0.378
HapMap-JPT Asian 88 IG 0.455 0.432 0.114 1.000 0.670 0.330
HapMap-YRI Sub-Saharan African 120 IG 0.267 0.483 0.250 1.000 0.508 0.492

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict		 Additional Freq. Data
0.498+/-0.031 1207 1002 0 0 ALFRED: The Allele Frequency Database

  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 .