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Reference SNP (refSNP) Cluster Report: rs4252129                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0068/822 (ExAC)
T=0.0024/12 (1000 Genomes)
T=0.0101/131 (GO-ESP)
T=0.0086/1074 (TOPMED)
HGVS Names
  • CM000668.2:g.160731873C>T
  • NC_000006.11:g.161152905C>T
  • NC_000006.12:g.160731873C>T
  • NG_016200.1:g.34681C>T
  • NM_000301.3:c.1567C>T
  • NP_000292.1:p.Arg523Trp
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss5607948 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4252129 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
ss5607948PGA-UW-FHCRC|PLG-032104byFreqfwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact12/23/0210/25/06111Genomicunknown
ss68998732PERLEGEN|PGP04771464byFreqfwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact01/30/0703/31/08127Genomicunknown
ss74817070AFFY|SNP_M-314139fwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact08/09/0708/09/07128Genomicunknown
ss160668053ILLUMINA|HumanOmni1-Quad_v1-0_B_rs4252129-128_B_F_1510672005fwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact08/04/0910/04/09131Genomicunknown
ss173703158ILLUMINA|Human1M-Duov3_B_rs4252129-128_B_F_1510672005fwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact10/01/0910/04/09132Genomicunknown
ss244299294ILLUMINA|CVDSNP55v1_A_rs4252129fwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact06/10/1006/10/10132Genomicunknown
ss3337835431000GENOMES|20100804_snps_5427084_chr6_161152905fwd/C/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact03/22/1103/22/11134Genomicunknown
ss342228126NHLBI-ESP|ESP2500-chr6-161152905byFreqfwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact03/25/1109/05/14134Genomicunknown
ss480910193ILLUMINA|HumanOmni2.5-4v1_B_rs4252129-128_B_F_1768755634fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag01/30/1210/28/16137Genomicunknown
ss480929237ILLUMINA|HumanOmniExpress-12v1_C_rs4252129-131_B_F_1857557840fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag01/30/1210/27/16137Genomicunknown
ss481886929ILLUMINA|HumanOmni1-Quad_v1-0_C_rs4252129-131_B_F_1865371767fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag01/30/1208/28/15146Genomicunknown
ss485250111ILLUMINA|HumanOmni2.5-4v1_D_rs4252129-131_B_F_1857557840fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag01/30/1210/28/16137Genomicunknown
ss4909385151000GENOMES|20110521_exome_446313_chr6_161152905fwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact02/10/1202/21/12137Genomicunknown
ss491394579EXOME_CHIP|nonsyn_110805_chr_6_161152905fwd/BC/Tcacagcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaagccact03/05/1203/05/12137Genomicunknown
ss491899912CLINSEQ_SNP|SNV-chr6-161072895byFreqfwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag03/06/1209/05/14137Genomicunknown
ss537221730ILLUMINA|HumanOmni5-4v1_B_rs4252129-131_B_F_1894867328fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag06/22/1208/29/15146Genomicunknown
ss778532299ILLUMINA|HumanOmni25Exome-8v1_A_rs4252129-131_B_F_1865371767fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/30/1307/09/15146Genomicunknown
ss780856216ILLUMINA|HumanOmni25Exome-8v1_A_exm593174-0_B_F_1921883105fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/30/1307/09/15146Genomicunknown
ss783071003ILLUMINA|HumanOmni2.5-4v1_H_rs4252129-131_B_F_1857557840fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/30/1307/28/15146Genomicunknown
ss783540295ILLUMINA|HumanOmniExpressExome-8v1_A_exm593174-0_B_F_1921883105fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/31/1306/19/15146Genomicunknown
ss784028824ILLUMINA|HumanOmniExpressExome-8v1_A_rs4252129-131_B_F_1894867328fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/31/1306/19/15146Genomicunknown
ss832329119ILLUMINA|HumanOmniExpress-12v1_H_rs4252129-131_B_F_1857557840fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag09/17/1306/19/15146Genomicunknown
ss833988840ILLUMINA|HumanOmni2.5-8v1_A_rs4252129-131_B_F_1865371767fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag09/18/1307/28/15146Genomicunknown
ss983732786EVA-GONL|EVA-GONL_rs4252129fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag04/23/1404/24/14142Genomicunknown
ss13231593851000GENOMES|PHASE3_V1_35246573fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag08/16/1408/16/14142Genomicunknown
ss1397478390HAMMER_LAB|HAMMER_LAB_rs4252129fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag09/30/1409/30/14146Genomicunknown
ss1581985530EVA_GENOME_DK|EVA_GENOME_DK_snv_rs4252129fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag02/19/1502/20/15144Genomicunknown
ss1584050267EVA_FINRISK|EVA_FINRISK_rs4252129fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag02/27/1502/27/15144Genomicunknown
ss1593309586EVA_DECODE|EVA_DECODE_6_161072895_1273635_rs4252129fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag03/02/1503/03/15144Genomicunknown
ss1617175653EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_6_161152905_19554528fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag03/04/1503/04/15144Genomicunknown
ss1660169686EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_6_161152905_19554528fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag03/04/1503/04/15144Genomicunknown
ss1688578812EVA_EXAC|EVA_EXAC_3628404fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag03/04/1503/04/15144Genomicunknown
ss1711149171EVA_MGP|EVA_XIMO_264931fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag03/09/1503/09/15144Genomicunknown
ss1752613318ILLUMINA|OmniExpressExome-8v1-1_B_exm593174-0_B_F_1921883105fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/27/1506/09/15146Genomicunknown
ss1752613319ILLUMINA|OmniExpressExome-8v1-1_B_rs4252129-131_B_F_1894867328fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/27/1506/09/15146Genomicunknown
ss1917813244ILLUMINA|HumanExome-12v1-1_B_exm593174-0_B_F_1921883105fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag10/16/1510/16/15147Genomicunknown
ss1946197420ILLUMINA|HumanCoreExome-12v1-0_C_exm593174-0_B_F_1921883105fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag10/29/1510/29/15147Genomicunknown
ss1958969471ILLUMINA|exm593174-0_B_F_1921883105fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag11/13/1511/13/15147Genomicunknown
ss2024153733JJLAB|SNP4656288fwd/BC/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag08/29/1608/30/16149Genomicunknown
ss2290227998HUMAN_LONGEVITY|HLI-6-160731873-C-Tfwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag11/18/1611/18/16150Genomicunknown
ss2458921095TOPMED|6_161152905_C/Tfwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag11/20/1611/20/16150Genomicunknown
ss2634540113ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SoL-rs4252129-131_T_R_2131fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag02/02/1702/02/17151Genomicunknown
ss2634540114ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs4252129-131_B_F_18948673fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag02/02/1702/02/17151Genomicunknown
ss2711097999ILLUMINA|Consortium-OncoArray_15047405_A_rs4252129-131_B_F_1894867328fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag03/22/1703/22/17151Genomicunknown
ss2736188225GNOMAD|exomes_rs4252129fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/17/1705/17/17151Genomicunknown
ss2747741545GNOMAD|coding_rs4252129fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/17/1705/17/17151Genomicunknown
ss2847622349GNOMAD|rs4252129fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/18/1705/18/17151Genomicunknown
ss2985394408AFFY|Axiom_PsorMich_Affx-28081750fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/24/1705/24/17151Genomicunknown
ss3000304147SWEGEN|NC_000006.11:g.161152905C>Tfwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag05/30/1705/30/17151Genomicunknown
ss3022687986ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm593174-0_B_F_1921883105fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag06/28/1706/28/17151Genomicunknown
ss3517615768TOPMED|TOPMed_freeze_5?chr6:160,731,873fwd/C/Tcattttcactccagagacaaatccagggcgggtctggaaaaaaatgtaag10/05/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4252129|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 ATTGCAGTTT CTGAGGAATG TGGCCCCTGA TTCTGTCATC CTAGAGAAAC CTGACATGAC
 TGTATTGATT CCATATCATC CTGGGTCTCT GTGGCTCTTC ATAATCATCC ATTTTTTCCC
 TGTACAGACT GTATGTTTGG GAATGGGAAA GGATACCGAG GCAAGAGGGC GACCACTGTT
 ACTGGGACGC CATGCCAGGA CTGGGCTGCC CAGGAGCCCC ATAGACACAG CATTTTCACT
 CCAGAGACAA ATCCA
 Y
 GGGCGGGTCT GGAAAAAAAT GTAAGCCACT TTGATTTGGA CTCTTTGGCC TTTTGCTCAC
 CAATCTTTGC AAACAGAATT GGTTCTGTGT TACAGAAAAT CTGACCTGGA CTGCTCTTTT
 TTGTAATGGG GGAGAGGGGA CAGAAGAAAA TATTGGAAAG GCATCAGGGG GCTAAGCTAG
 AATATAATTG GCCTTAGTAT GGAAAGTACA AGCAGCACAG GCCAGGAAAC CTCCACACAT
 GTGAGGGTTC TCAGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000006.9
dbSNP Blast Analysis
UniGene Cluster ID
143436
3D structure mapping
NP_000292  

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1323159385EAS 1008AF 1.00000000
EUR 1006AF 0.991099950.00890000
AFR 1322AF 1.00000000
AMR 694AF 0.995700000.00430000
SAS 978AF 1.00000000
ss1688578812ExAc_Aggregated_Populations121412AF 0.993229690.00677034
ss342228126ESP_Cohort_Populations 4542GF0.981505930.018053720.000440330.099721000.990532820.00946719
ss491899912CSAgilent 1323GF0.976000010.02400000 1.000000000.987999980.01200000
ss5607948PGA-AFRICAN-PANELAfrican American 48IG0.958333310.04166667 1.000000000.979166690.02083333
PGA-EUROPEAN-PANELEuropean 46IG1.00000000 1.00000000
HapMap-CEUEuropean 120IG0.966666640.03333334 1.000000000.983333350.01666667
HapMap-HCBAsian 90IG1.00000000 1.00000000
HapMap-JPTAsian 90IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.013+/-0.0810000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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