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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1563102          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_018958.2:c.757G>C
NP_061831.2:p.Gly253Arg
NT_026446.13:g.1356570G>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 ss2406908 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1563102 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
ss2406908TSC-CSHL|TSC0453548byFreqfwd/TC/Gcacagccaggccggatgtgcccggcatcttgaaagcctgatccggatgcaacagcgcccc10/20/0005/16/0488Genomic95 %
ss3661108SC_JCM|AC019094.6_110381fwd/TC/Gcacagccaggccggatgtgcccggcatcttgaaagcctgatccggatgcaacagcgcccc09/24/0110/10/03100Genomicunknown
ss4970600YUSUKE|IMS-JST140694byFreqrev/BC/Gggggcgctgttgcatccggatcaggctttcaagatgccgggcacatccggcctggctgtg08/12/0210/10/03108Genomicunknown
ss24801420SEQUENOM|sqnm160765fwd/TC/Gcacagccaggccggatgtgcccggcatcttgaaagcctgatccggatgcaacagcgcccc06/18/0406/18/04123cDNAunknown
ss48409428APPLERA_GI|hCV7515437byFreqfwd/C/Gcacagccaggccggatgtgcccggcatcttgaaagcctgatccggatgcaacagcgcccc09/28/0511/03/06126Genomicunknown
ss90095244BCMHGSC_JDW|JWB-0831190fwd/C/Gcacagccaggccggatgtgcccggcatcttgaaagcctgatccggatgcaacagcgcccc02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1563102|allelePos=260|totalLen=713|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=129
 GGTGCAGATC GAAGGGGAGG ATGACGAGAA AAGGACCCCC CTTAGCAGCG GAGAAGCATC
 GTCCACATCC AGGTCCCAGG GCACCCAGGG AGACGTGGCC TCCTTCAGAT GCAGCCCTGG
 GCCTCTGGAG GGAAATGTCT ACCACAAGTT CTCAGAAAAC AGCATGAGTG AGAAGGCCCA
 GGCGTCTCCA GCGAGCTCCT GCTTGGAAGG CCCTGCCATG CCCAGCACAC ACAGCCAGGC
 CGGATGTGCC CGGCATCTT
 S
 GAAAGCCTGA TCCGGATGCA ACAGCGCCCC CTGAGCCAGC CGTTGGCTGC TCCCTGCTGC
 AGCAGAAGTT GGCTGCGGAA GTGCTGAATG AAGAGCCACC GCCCAGCTCC CTAGGCTTGC
 CGATTCCGCT GATGTCCGGA AAGAGGATGC CTGATGAGAA GCCTTTCTGT ATTCCTCCAA
 GGAGCGCTGC TCCTCCCAGA GCTGCCCGCA ACAGGCCCTG CAAAAGGAAA ATGTCGATTC
 CATTGCTGCT GCCGCTGCCC CCTTCACTGC CATTGCTGTG GGATCGAGGT GAGCTTCCCC
 CACCTGCTAA GCTCCCCTGC CTGTCTGTTG AGGGAGACCT ACACACCTTG GAGAAGAGCC
 CTGAGTATAA AAGGAATAGC AGAATCTTGG AGGATAAAAC AGAGACCATG ACAAACAGCA
 GCATCACCCA GCCTGCCCCT TCTTTCTCCC AAC

  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
dbSTS GenBank
sqnm160765 NT_010178.1 AF179681
dbSNP Blast Analysis
UniGene Cluster ID
451286

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 G/G
 HWP C
 G
ss2406908 CEPH 184 AF 0.220 0.780
HapMap-CEU European 120 IG 0.100 0.400 0.500 0.752 0.300 0.700
HapMap-HCB Asian 90 IG 0.333 0.400 0.267 0.200 0.533 0.467
HapMap-JPT Asian 88 IG 0.205 0.523 0.273 0.752 0.466 0.534
HapMap-YRI Sub-Saharan African 120 IG 1.000 1.000
ss48409428 AGI_ASP population multiple 62 IG 0.290 0.710 0.371 0.145 0.855
ss4970600 JBIC-allele 1486 AF 0.470 0.530

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.402+/-0.198 557 441 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
byClusterbyFreqwithHapMapFreq UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .