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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs997568          
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
NT_004487.18:g.34672746A>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 ss44067799 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs997568 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
ss1456239TSC-CSHL|TSC0002990byFreqfwd/BC/Tggagccaactgggaggagggaaatgagaacgggggaaacacgggggagactcaacctcat09/07/0010/25/0686Genomic95 %
ss5883595SC_JCM|NT_004487.12_9300097rev/TA/Gatgaggttgagtctcccccgtgtttcccccgttctcatttccctcctcccagttggctcc01/10/0310/10/03111Genomicunknown
ss16421438CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_004487.16_13230889rev/TA/Gatgaggttgagtctcccccgtgtttcccccgttctcatttccctcctcccagttggctcc02/17/0403/04/04120Genomicunknown
ss19850632CSHL-HAPMAP|CSHL-HuFF-200402.chr1.NT_004487.16_13230889rev/TA/Gatgaggttgagtctcccccgtgtttcccccgttctcatttccctcctcccagttggctcc02/21/0403/04/04120Genomicunknown
ss44067799ABI|hCV2867629rev/TA/Gatgaggttgagtctcccccgtgtttcccccgttctcatttccctcctcccagttggctcc07/18/0507/18/05126Genomicunknown
ss1087617191000GENOMES|CEU.trio.12.15.2008_201874_chr1_182449015rev/TA/Gatgaggttgagtctcccccgtgtttcccccgttctcatttccctcctcccagttggctcc12/15/0812/16/08130Genomicunknown
ss1114606511000GENOMES|NA19240_2008_12_16_186119_chr1_182449015rev/TA/Gatgaggttgagtctcccccgtgtttcccccgttctcatttccctcctcccagttggctcc12/16/0812/17/08130Genomicunknown
ss119125604ILLUMINA-UK|NA18507_000184223_NCBI36.1_chr1_182449015rev/TA/Gatgaggttgagtctcccccgtgtttcccccgttctcatttccctcctcccagttggctcc01/21/0901/22/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs997568|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TGATGGATTA ATGACTCTGG TTTTATGAGA TTGGTTGTAA GGAGTCATTG CAAAATCTTA
 GGGAAGGGAA GTCACACAAT TATAGTATGT TTGCTGAGGG ACTGAGGAAG AGAGAAAGCC
 ATCACCTCCT CTACCCTCCA TCAGGGGAGA CTGTCAAATA AACAGAAGCT TTAAAATATA
 TACTTTGTAG GAGACTAGGG CGAAAAAGGA ATACGGCTGT GGAAGGACTC CTAGTGTGTC
 TGAAGCTACT CTGTGGTGGG AGGCTGGTGT GGAGCCAACT GGGAGGAGGG AAATGAGAAC
 Y
 GGGGGAAACA CGGGGGAGAC TCAACCTCAT AGACCCAAGG AGGCCAACTA GGGAAGGGAA
 GATGGGCCTG AAAGTGAAAG GCCAGACTTA AGTCCTAGCT CTGCCCTTTC CCAGCAGGGA
 GGCCTCAGGC AAGTCCTGAA AGCTGTGGGA GGTTTTGCTT CCTCATTCCT AAGATGGCAG
 TCATGGTCCC TGCTTCAAAA GCTGCTGAGG TAAAAATAAA TGAGGTCACG TGCATGAAAT
 CCCTTGACAA ATGCCAAGTT ATCTGGGAAA TAGTAGAAGC GGTGTTTTAA TTATTTTTGC

  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_004487.12 AL158011.2 AL354657.2
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotypesAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source HWP C
 T
ss1456239 TSC_42_AA 82 AF 0.317 0.683
TSC_42_C 82 AF 0.402 0.598
TSC_42_A 78 AF 0.474 0.526

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.479+/-0.101 0 0 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
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .