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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:80/147
Map to Genome Build:107/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
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:C=0.1843/5332 (ExAC)
C=0.1506/754 (1000 Genomes)
C=0.1416/1769 (GO-ESP)
HGVS Names
  • NC_000019.10:g.44908684T>C
  • NC_000019.9:g.45411941T>C
  • NG_007084.2:g.7903T>C
  • NM_000041.3:c.388T>C
  • NM_001302688.1:c.466T>C
  • NM_001302689.1:c.388T>C
  • NM_001302690.1:c.388T>C
  • NM_001302691.1:c.388T>C
  • NP_000032.1:p.Cys130Arg
  • NP_001289617.1:p.Cys156Arg
  • NP_001289618.1:p.Cys130Arg
  • NP_001289619.1:p.Cys130Arg
  • NP_001289620.1:p.Cys130Arg
  • XM_005258867.1:c.466T>C
  • XM_005258868.1:c.388T>C
  • XP_005258924.1:p.Cys156Arg
  • XP_005258925.1:p.Cys130Arg
Links , Linkout
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 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_17680159byFreqfwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg09/20/0709/05/14129Genomicunknown
ss80743998KRIBB_YJKIM|KHS1001043byFreqfwd/BC/Tgccmggctgggcgcggacatggaggacgtggcggcmgcctggtgcagtaccrcggcgagg11/26/0709/05/14130Genomicunknown
ss96308980HUMANGENOME_JCVI|1103691153316fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg03/26/0803/26/08130Genomicunknown
ss107936537RSG_UW|APOE-004874byFreqfwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg12/08/0809/05/14130Genomicunknown
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/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg01/30/1208/28/15146Genomicunknown
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/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg06/22/1208/29/15146Genomicunknown
ss537712916NCBI-CURATED-RECORDS|32902_1fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg07/19/1201/04/13137Genomicunknown
ss661874596SSMP|19_45411941fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg12/14/1202/14/15138Genomicunknown
ss713519649NHLBI-ESP|ESP6500SI-chr19-45411941fwd/BC/Tgcccggctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcggcgagg02/20/1302/20/13138Genomicunknown
ss780608662ILLUMINA|HumanOmni25Exome-8v1_A_kgp9680313-0_B_F_1816363075fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg05/30/1307/10/15142Genomicunknown
ss782605255ILLUMINA|HumanOmni2.5-4v1_H_kgp9680313-0_B_F_1816363075fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg05/30/1307/29/15142Genomicunknown
ss836101974ILLUMINA|HumanOmni2.5-8v1_A_kgp9680313-0_B_F_1816363075fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg09/18/1307/29/15142Genomicunknown
ss974506672JMKIDD_LAB|KhoeSan_Exomes_chr19_45411941fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg03/06/1403/06/14142Genomicunknown
ss994339187EVA-GONL|EVA-GONL_rs429358fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg04/23/1405/01/14142Genomicunknown
ss1067590770JMKIDD_LAB|HGDP_exomes_chr19_45411941fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg07/09/1407/09/14142Genomicunknown
ss13633261841000GENOMES|PHASE3_V1_77055807fwd/C/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg08/16/1408/16/14142Genomicunknown
ss1578653635EVA_GENOME_DK|EVA_GENOME_DK_snv_rs429358fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg02/19/1502/20/15144Genomicunknown
ss1638043657EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_19_45411941_42493851fwd/C/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg03/04/1503/04/15144Genomicunknown
ss1681037690EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_19_45411941_42493851fwd/C/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg03/04/1503/04/15144Genomicunknown
ss1693665397EVA_EXAC|EVA_EXAC_9103417fwd/C/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg03/04/1503/04/15144Genomicunknown
ss1698394130EVA_DECODE|EVA_DECODE_19_50103781_334935_rs429358fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg03/02/1503/05/15144Genomicunknown
ss1937835821WEILL_CORNELL_DGM|SNV:chr19:45411941fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg10/16/1510/19/15147Genomicunknown
ss1959869660ILLUMINA|19:45411941-A-G-0_B_F_2304705815fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869661ILLUMINA|19:45411941-A-G-R1-0_B_F_2304705805fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869662ILLUMINA|19:45411941-A-G-R2-0_B_F_2304705807fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869663ILLUMINA|19:45411941-A-G-R3-0_B_F_2304705809fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869665ILLUMINA|19:45411941-A-G-R4-0_B_F_2304705811fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869666ILLUMINA|19:45411941-A-G-R5-0_B_F_2304705813fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869667ILLUMINA|19:45411941-T-C-0_B_F_2304248373fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869668ILLUMINA|19:45411941-T-C-F1-0_B_F_2304705774fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869669ILLUMINA|19:45411941-T-C-F10-0_B_F_2304705792fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869670ILLUMINA|19:45411941-T-C-F11-0_B_F_2304705794fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869671ILLUMINA|19:45411941-T-C-F12-0_B_F_2304705796fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869672ILLUMINA|19:45411941-T-C-F13-0_B_F_2304705798fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869673ILLUMINA|19:45411941-T-C-F15-0_B_F_2304705802fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869675ILLUMINA|19:45411941-T-C-F2-0_B_F_2304705776fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869676ILLUMINA|19:45411941-T-C-F3-0_B_F_2304705778fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869677ILLUMINA|19:45411941-T-C-F5-0_B_F_2304705782fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869678ILLUMINA|19:45411941-T-C-F6-0_B_F_2304705784fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869679ILLUMINA|19:45411941-T-C-F7-0_B_F_2304705786fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown
ss1959869680ILLUMINA|19:45411941-T-C-F9-0_B_F_2304705790fwd/BC/Tgctgggcgcggacatggaggacgtggcggccgcctggtgcagtaccgcgg11/13/1511/13/15147Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs429358|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=147
 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 (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
ss107936537ABECASIS_CLINICAL_PANEL 752AF 0.106382980.89361703
ss12568607American Caucasians 1858AF 0.148999990.85100001
ss132769779ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss1363326184EAS 1008AF 0.086300000.91369998
EUR 1006AF 0.155099990.84490001
AFR 1322AF 0.267800000.73219997
AMR 694AF 0.103700000.89630002
SAS 978AF 0.086900000.91310000
ss168243995CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss1693665397ExAc_Aggregated_Populations113556AF 0.100232480.89976752
ss228156553pilot_1_YRI_low_coverage_panel 118AF 0.144067790.85593218
ss237689596pilot_1_CEU_low_coverage_panel 120AF 0.091666670.90833336
ss44158325CABG_NORTHAMERICAN 2120GF0.023584910.262264160.714150971.000000000.154716980.84528303
ss76884559HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 88IG 0.022727270.977272751.000000000.011363640.98863637
HapMap-YRISub-Saharan African 120IG 0.033333340.966666641.000000000.016666670.98333335
ss80743998KHP1 178AF0.011235960.157303380.831460650.751830000.089887640.91011238
KHP_Korean 178IG0.011235960.157303380.831460650.751830000.089887640.91011238
ss870163MDECODE-1 48AF 0.120000000.88000005
MDECODE-2 48AF 0.230000000.76999998
MDECODE-3 48AF 0.100000010.90000004
MDECODE-4 48AF 0.100000010.90000004
ss96308980J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.301+/-0.24544438600ALFRED: 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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