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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1020636          
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:T
Clinical Association:unknown
HGVS Names
NM_206943.1:c.565+12249C>A
NT_022184.14:g.12002194A>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 ss1484932 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1020636 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
ss1484932TSC-CSHL|TSC0224883byFreqfwd/BC/Tgcaatctgggcaccaggcaggtggtcaggcatgagaataatttgtgtgtggacttgggta09/07/0004/07/0486Genomic95 %
ss44221118ABI|hCV8898270byFreqrev/TA/Gtacccaagtccacacacaaattattctcatgcctgaccacctgcctggtgcccagattgc07/18/0511/03/06126Genomicunknown
ss83785879HGSV|Cor18555_SNV_20070510.chr2_33097912rev/TA/Gtacccaagtccacacacaaattattctcatgcctgaccacctgcctggtgcccagattgc11/27/0712/05/07130Genomicunknown
ss85894545HGSV|Cor18517_SNV_20070510.chr2_33097912rev/TA/Gtacccaagtccacacacaaattattctcatgcctgaccacctgcctggtgcccagattgc12/06/0712/10/07130Genomicunknown
ss106079731BGI|BGI_rs1020636rev/TA/Gtacccaagtccacacacaaattattctcatgcctgaccacctgcctggtgcccagattgc09/13/0806/17/09130Genomicunknown
ss1093806181000GENOMES|CEU.trio.12.15.2008_346017_chr2_33039765rev/TA/Gtacccaagtccacacacaaattattctcatgcctgaccacctgcctggtgcccagattgc12/15/0812/16/08130Genomicunknown
ss1100384461000GENOMES|NA19240_2008_12_16_313069_chr2_33039765rev/TA/Gtacccaagtccacacacaaattattctcatgcctgaccacctgcctggtgcccagattgc12/16/0812/17/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1020636|allelePos=171|totalLen=625|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 AATAGTGACC AGTGACTTGG CTTTCTTCAC CCTCACACTT TCATCCTAAA CCGCAGCCTC
 GCAGCTCCCT GCTGAGGGTC TTGCCTTTCC ACGAGAGCTC GGCAGAGACC CGGAGGTCCA
 GTCAGCACAA GGCTGGTCTG GCAATCTGGG CACCAGGCAG GTGGTCAGGC
 Y
 ATGAGAATAA TTTGTGTGTG GACTTGGGTA CTTCACTGTT CCACGTGCAG TTTTTCTCAT
 CAATAAAAAA TAGCAATCAA AGTGATCTAA TGAATTTTCT ACGTAAGATA TTTTTCCATG
 CCTTAAAAAA TACTAAATCC TTTATTTTCT TTAATTTCTT AGTAATAAAA TACACTTGCA
 TGCACTCGTG TTTTATAGTA CTTGTGTTGA CTGTGCTTGT GTTGTACAGT CCCCTCTTGT
 TATCTTATCT GTGGCCTCAC ACAGCCTAGA AGACTTGACT TGGGATCCAA CCCTATCTTA
 TGTCACCTAT TACAGCAGCC CTCACTGACA ACCCAACGAT AATGACCTAT GTTCCCACAA
 CAAGCCAGGC CTATCCCCAC TCCAAGGCCT TTGTGCTAGC CATTCTGTTG GCCTAAAATA
 CTCTTCTCTC AGACCCTTTC ATATCACACA GGCC

  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
AC019180.6 AC020598.4 AL133244.1
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
ss1484932 TSC_42_AA 84 AF 0.298 0.702
TSC_42_C 80 AF 0.475 0.525
TSC_42_A 82 AF 0.707 0.293
HapMap-CEU European 120 IG 0.183 0.400 0.417 0.251 0.383 0.617
HapMap-HCB Asian 90 IG 0.444 0.378 0.178 0.251 0.633 0.367
HapMap-JPT Asian 88 IG 0.364 0.545 0.091 0.251 0.636 0.364
HapMap-YRI Sub-Saharan African 120 IG 0.050 0.200 0.750 0.100 0.150 0.850
ss44221118 AoD_African_American 90 AF 0.300 0.700
AoD_Caucasian 92 AF 0.370 0.630

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.488+/-0.076 525 409 0 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .