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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2126852          
refSNP ID: rs2126852
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:96/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_001008925.1:c.*1083A>G
NM_001009922.1:c.*902A>G
NM_015436.2:c.*902A>G
NT_016354.18:g.954567T>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 ss3050234 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2126852 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
ss3050234TSC-CSHL|TSC1134485byFreqfwd/TA/Ggtacattctattgttcatcatatttgatcatgtactcatttttctttatgcaaggagtgg06/07/0110/25/0696Genomicunknown
ss6188417SC_JCM|NT_022760.11_166655rev/BC/Tccactccttgcataaagaaaaatgagtacatgatcaaatatgatgaacaatagaatgtac01/10/0310/10/03111Genomicunknown
ss22067100SSAHASNP|WGSA-200403-chr4.chr4.NT_016354.16_901551rev/BC/Tccactccttgcataaagaaaaatgagtacatgatcaaatatgatgaacaatagaatgtac03/20/0403/20/04121Genomicunknown
ss23903531PERLEGEN|afd2953777byFreqrev/BC/Tccactccttgcataaagaaaaatgagtacatgatcaaatatgatgaacaatagaatgtac08/10/0409/13/04123Genomicunknown
ss42221343ABI|hCV15825937rev/BC/Tccactccttgcataaagaaaaatgagtacatgatcaaatatgatgaacaatagaatgtac07/17/0507/17/05126Genomicunknown
ss67226565ILLUMINA|HumanHap550v1.1_rs2126852fwd/TA/Ggtacattctattgttcatcatatttgatcatgtactcatttttctttatgcaaggagtgg11/14/0611/14/06127Genomicunknown
ss67621545ILLUMINA|HumanHap650Yv1.0_rs2126852fwd/TA/Ggtacattctattgttcatcatatttgatcatgtactcatttttctttatgcaaggagtgg11/14/0611/14/06127Genomicunknown
ss68196967ILLUMINA|HumanHap250Sv1.0_rs2126852fwd/TA/Ggtacattctattgttcatcatatttgatcatgtactcatttttctttatgcaaggagtgg12/06/0612/07/06127Genomicunknown
ss70704866ILLUMINA|HumanHap550v3.0__rs2126852rev/BC/Tccactccttgcataaagaaaaatgagtacatgatcaaatatgatgaacaatagaatgtac04/20/0703/30/08130Genomicunknown
ss71271443ILLUMINA|HumanHap650Yv3.0_rs2126852fwd/TA/Ggtacattctattgttcatcatatttgatcatgtactcatttttctttatgcaaggagtgg04/23/0704/23/07127Genomicunknown
ss75818041ILLUMINA|ILMN_Human_1M_rs2126852fwd/TA/Ggtacattctattgttcatcatatttgatcatgtactcatttttctttatgcaaggagtgg08/28/0708/29/07129Genomicunknown
ss83977294KRIBB_YJKIM|KHS590211fwd/TA/Ggtacattctattgttcatcatatttgatcatgtactcatttttctttatgcaaggagtgg12/04/0712/06/07130Genomicunknown
ss92647691BCMHGSC_JDW|JWB-1803939rev/BC/Tccactccttgcataaagaaaaatgagtacatgatcaaatatgatgaacaatagaatgtac02/26/0803/03/08129Genomicunknown
ss1080554931000GENOMES|CEU.trio.12.15.2008_1013230_chr4_76625870rev/BC/Tccactccttgcataaagaaaaatgagtacatgatcaaatatgatgaacaatagaatgtac12/15/0812/15/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2126852|allelePos=452|totalLen=691|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TAGAATTTTC TAAGACAGTC CTCTGGATCC TCTAAATGTG AATTTTGATG TAATAACTGC
 TAATAAAATT ATATTGAAAC TGTTTTATAG AAAGTTTTTT CCAAAGTTTT CTATGTTTGG
 CTCAATTAGG GCAGTATCAT CAGTTCTATA ATGTAAAAGA AATTTTCTTT CTTTTGAGGT
 ATTCCATAAA AGTAGTTGGG AAAATTATTA TGTAAAATAA TAAGACTCTT CCAAAGCCTT
 AATAAAAACA TCAACATTGA AAACAGTTTT TTTTAGGTTG CCCAAAATTA TTTCTTCAAA
 GAGTCATTCa ttccttcatt tagcaagtat ttattgagca actgctatgt ggcagatatg
 tttctagatg ctgtagagac aacagtgaac aataaagata aaagtccttg tcctcacagc
 agtacattct attgTTCATC ATATTTGATC A
 R
 TGTACTCATT TTTCTTTATG CAAGGAGTGG ATGTCTTATT GTAAATGAAT AGAATATTTC
 TTCCCTAAGC GTGTGAAAAT AGGGGATGGA TGAGTGGGAA GGGCATGGGA TATTCCTGGC
 AAGATCTCTG ATTTCATAAT ACTTTTTTGG GCTCATGTAG TGGAATTAAA TATACCTCTT
 ACTTCAGGAA CAAAGTTAAC AAATATGTTT GATGATCCAG CCGACTTTGA CACTGTTAT

  GeneView back to top
GeneView via analysis of contig annotation: RCHY1 ring finger and CHY zinc finger domain containing 1
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_016354->NM_001008925
svfunction
referenceNT_016354->NM_001009922
svfunction
referenceNT_016354->NM_015436
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_016354->NM_001008925->954567reverse18183' UTR
referenceNT_016354->NM_001009922->954567reverse17933' UTR
referenceNT_016354->NM_015436->954567reverse18203' UTR

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2126852 maps exactly once on NCBI human chromosome 4
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
4NW_001838915.191491772153367minusTalt_assembly_8HuRefHuRefview451
4NW_922162.12352795273702978minusTalt_assembly_1CeleraCeleraview451
4NT_016354.1895456776625870minusTref_assemblyreferencereferenceview451

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022760.11
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_001008925.1 NM_001009922.1 NM_015436.2
UniGene Cluster ID
48297

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss23903531AFD_EUR_PANELEuropean 44IG 0.455 0.500 0.045 0.371 0.705 0.295
AFD_AFR_PANELAfrican American 40IG 0.800 0.150 0.050 0.200 0.875 0.125
AFD_CHN_PANELAsian 46IG 0.478 0.391 0.130 0.655 0.674 0.326
ss3050234HapMap-CEUEuropean 114IG 0.474 0.421 0.105 1.000 0.684 0.316
HapMap-HCBAsian 86IG 0.558 0.419 0.023 0.273 0.767 0.233
HapMap-JPTAsian 86IG 0.674 0.256 0.070 0.251 0.802 0.198
HapMap-YRISub-Saharan African 112IG 0.625 0.357 0.018 0.343 0.804 0.196

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.367+/-0.22133226090

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .