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Reference SNP (refSNP) Cluster Report: rs429358                 ** With pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:80/138
Map to Genome Build:37.5/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMed
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:C:germline
T:germline
Ancestral Allele:C
Clinical Channel:link to VariationViewerlink to OMIM
Clinical Significance:With pathogenic allele [ClinVar]
MAF/MinorAlleleCount:C=0.149/325
MAF Source:1000 Genomes
HGVS Names
NC_000019.9:g.45411941T>C
NG_007084.2:g.7903T>C
NM_000041.2:c.388T>C
NP_000032.1:p.Cys130Arg
NT_011109.16:g.17680159T>C
Links , Linkout
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' or 'Contig Pos' column value to see variation in NCBI sequence 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 ss76884559 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs429358 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
ss569295SC_JCM|AC011481.2_65149fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg07/12/0010/10/0380Genomicunknown
ss803061SC_JCM|AF050154.1_21250fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg07/27/0010/10/0385Genomicunknown
ss870163DEBNICK|ae3937byFreqfwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg08/29/0004/07/0486Genomicunknown
ss2419938HGBASE|SNP000002328fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/07/0010/10/0389Genomicunknown
ss12568607CUORCGL|SNP1byFreqfwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg07/08/0310/25/06117Genomicunknown
ss16231123CGAP-GAI|1470380fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg11/18/0311/22/03120cDNAunknown
ss21518782SSAHASNP|WGSA-200403-chr19.chr19.NT_011109.15_17680159fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg03/20/0403/20/04121Genomicunknown
ss24811489SEQUENOM|sqnm198707fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg06/18/0406/18/04123cDNAunknown
ss44158325ABI|hCV3084793byFreqfwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg07/18/0511/03/06126Genomicunknown
ss76884559SI_EXO|NT_011109.15_17680159fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg09/20/0709/20/07129Genomicunknown
ss80743998KRIBB_YJKIM|KHS1001043fwd/BC/Tgccmggctgggcgcggacatggaggacgtggcggcmgcctggtgcagtaccrcggcgagg11/26/0711/26/07130Genomicunknown
ss96308980HUMANGENOME_JCVI|1103691153316fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg03/26/0803/26/08130Genomicunknown
ss107936537RSG_UW|APOE-004874fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg12/08/0812/08/08130Genomicunknown
ss132769779ENSEMBL|ENSSNP1536174fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg12/08/0810/15/09131Genomicunknown
ss159740185SEATTLESEQ|APOE-50103781fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg07/10/0907/10/09131Genomicunknown
ss160670648ILLUMINA|HumanOmni1-Quad_v1-0_B_rs429358-128_B_F_1561710586fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg08/04/0910/04/09131Genomicunknown
ss168243995COMPLETE_GENOMICS|NA07022_36_chr19_50103781fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg09/30/0909/30/09132Genomicunknown
ss181341884PAGE_STUDY|PAGE_WHI_rs429358rev/TA/Gcctcgccgcggtactgcaccaggcggccgccacgtcctccatgtccgcgcccagccgggc12/04/0912/04/09132Genomicunknown
ss2281565531000GENOMES|pilot_1_YRI_9966236_chr19_50103781fwd/C/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg04/22/1004/22/10132Genomicunknown
ss2376895961000GENOMES|pilot_1_CEU_7294225_chr19_50103781fwd/C/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg05/01/1005/01/10132Genomicunknown
ss244239676OMICIA|2010_April_001_004_APOE_107741_0008fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg05/27/1005/28/10132Genomicunknown
ss275517967OMIM-CURATED-RECORDS|518fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg12/03/1012/03/10133Genomicunknown
ss410828263ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr19_50103781fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg06/07/1106/07/11135Genomicunknown
ss469414605PAGE_STUDY|PAGE_MEC_Y1_rs429358fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg09/26/1109/26/11137Genomicunknown
ss481897219ILLUMINA|HumanOmni1-Quad_v1-0_C_rs429358-131_B_F_1858946940fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg01/30/1202/01/12137Genomicunknown
ss483834108ILLUMINA|HumanOmni2.5-4v1_B_SNP19-50103781-0_B_F_1622613995fwd/BC/Tgcccggctgggcgcggacatggaggacgtggnnnnngcctggtgcagtaccgcggcgagg01/30/1202/03/12137Genomicunknown
ss484318107ILLUMINA|HumanOmni2.5-4v1_D_kgp9680313-0_B_F_1816363075fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg01/30/1202/03/12137Genomicunknown
ss4911617511000GENOMES|20110521_exome_669549_chr19_45411941fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg02/10/1202/22/12137Genomicunknown
ss491549548EXOME_CHIP|nonsyn_265774_chr_19_45411941fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg03/05/1203/06/12137Genomicunknown
ss536501696ILLUMINA|HumanOmni5-4v1_B__kgp9680313-0_B_F_1816363075fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg06/22/1206/30/12138Genomicunknown
ss537712916NCBI-CURATED-RECORDS|32902_1fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg07/19/1201/04/13136Genomicunknown
ss661874596SSMP|19_45411941fwd/BC/Tgcccggctgggcgcggacatggaggacgtgcggccgcctggtgcagtaccgcggcgaggt12/14/1212/17/12138Genomicunknown
ss713519649NHLBI-ESP|ESP6500SI-chr19-45411941fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg02/20/1302/20/13138Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs429358|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=138
 CCTCGGCCTC CCAAAGTGCT GGGATTAGAG GCATGAGCCA CCTTGCCCGG CCTCCTAGCT
 CCTTCTTCGT CTCTGCCTCT GCCCTCTGCA TCTGCTCTCT GCATCTGTCT CTGTCTCCTT
 CTCTCGGCCT CTGCCCCGTT CCTTCTCTCC CTCTTGGGTC TCTCTGGCTC ATCCCCATCT
 CGCCCGCCCC ATCCCAGCCC TTCTCCCCGC CTCCCACTGT GCGACACCCT CCCGCCCTCT
 CGGCCGCAGG GCGCTGATGG ACGAGACCAT GAAGGAGTTG AAGGCCTACA AATCGGAACT
 GGAGGAACAA CTGACCCCGG TGGCGGAGGA GACGCGGGCA CGGCTGTCCA AGGAGCTGCA
 GGCGGCGCAG GCCCGGCTGG GCGCGGACAT GGAGGACGTG
 Y
 GCGGCCGCCT GGTGCAGTAC CGCGGCGAGG TGCAGGCCAT GCTCGGCCAG AGCACCGAGG
 AGCTGCGGGT GCGCCTCGCC TCCCACCTGC GCAAGCTGCG TAAGCGGCTC CTCCGCGATG
 CCGATGACCT GCAGAAGCGC CTGGCAGTGT ACCAGGCCGG GGCCCGCGAG GGCGCCGAGC
 GCGGCCTCAG CGCCATCCGC GAGCGCCTGG GGCCCCTGGT GGAACAGGGC CGCGTGCGGG
 CCGCCACTGT GGGCTCCCTG GCCGGCCAGC CGCTACAGGA GCGGGCCCAG GCCTGGGGCG
 AGCGGCTGCG CGCGCGGATG GAGGAGATGG GCAGCCGGAC CCGCGACCGC CTGGACGAGG
 TGAAGGAGCA GGTGGCGGAG GTGCGCGCCA AGCTGGAGGA

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm198707 NT_011109.15 ABBA01040892 AC011481 AC021988 BQ712095
dbSNP Blast Analysis
UniGene Cluster ID
515465
3D structure mapping
NP_000032  
OMIM
107741.0008
107741.0015
107741.0016

  Population Diversity (in rs orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss107936537ABECASIS_CLINICAL_PANEL 752AF 0.106 0.894
ss12568607American Caucasians 1858AF 0.149 0.851
ss132769779ENSEMBL_Venter 2IG 1.000 0.500 0.500
ss168243995CEUEuropean 2IG 1.000 0.500 0.500
ss228156553pilot_1_YRI_low_coverage_panel 118AF 0.144 0.856
ss237689596pilot_1_CEU_low_coverage_panel 120AF 0.092 0.908
ss44158325CABG_NORTHAMERICAN 2120GF 0.024 0.262 0.714 1.000 0.155 0.845
ss76884559HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 88IG 0.023 0.977 1.000 0.011 0.989
HapMap-YRISub-Saharan African 120IG 0.033 0.967 1.000 0.017 0.983
ss80743998KHP1 178AF 0.011 0.157 0.831 0.752 0.090 0.910
KHP_Korean 178IG 0.011 0.157 0.831 0.752 0.090 0.910
ss870163MDECODE-1 48AF 0.120 0.880
MDECODE-2 48AF 0.230 0.770
MDECODE-3 48AF 0.100 0.900
MDECODE-4 48AF 0.100 0.900
ss96308980J. Craig Venter 2IG 1.000 0.500 0.500

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.254+/-0.25044438600ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNYES

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