NCBI
dbSNP
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This legacy RefSNP page contains old data from dbSNP build 151 (March 2018) and is no longer maintained. Please update your links and bookmarks to use the re-designed RefSNP Report page.
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Reference SNP (refSNP) Cluster Report: rs9424290                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
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=0.2218/1111 (1000 Genomes)
T=0.1020/12807 (TOPMED)
HGVS Names
  • CM000663.2:g.3825445C>T
  • NC_000001.10:g.3742009C>T
  • NC_000001.11:g.3825445C>T
  • NG_046726.1:g.36789G>A
  • NM_014704.3:c.2364+313G>A
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 ss275691501 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9424290 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
ss12992583SC_SNP|NT_004321.15_1048783byFreqfwd/BC/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa10/22/0310/25/06119Genomicunknown
ss68756691PERLEGEN|PGP06896078byFreqfwd/BC/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa01/30/0703/31/08127Genomicunknown
ss105114961BGI|BGI_rs9424290fwd/BC/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa08/06/0806/16/09131Genomicunknown
ss160986542ILLUMINA|HumanOmni1-Quad_v1-0_B_rs9424290-128_B_F_1545057022fwd/BC/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa08/04/0910/05/09131Genomicunknown
ss205184305BCM-HGSC-SUB|BCM_CMT_1011-72313fwd/BC/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa03/15/1003/15/10132Genomicunknown
ss2182033281000GENOMES|pilot_1_YRI_13011_chr1_3731869fwd/C/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa04/22/1004/22/10132Genomicunknown
ss2304042071000GENOMES|pilot_1_CEU_8836_chr1_3731869fwd/C/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa05/01/1005/01/10132Genomicunknown
ss2381230861000GENOMES|pilot_1_CHB+JPT_8163_chr1_3731869fwd/C/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa05/01/1005/01/10132Genomicunknown
ss275691501GMI|GMI_AK_SNP_11662fwd/C/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa12/16/1012/16/10137Genomicunknown
ss283991035GMI|GMI_NA10851_SNP_3801fwd/C/Tggacactataaagcaagaaatccaacatgagccacatggttccgtttctacaaagctcaa12/17/1012/17/10138Genomicunknown
ss481897499ILLUMINA|HumanOmni2.5-4v1_B_rs9424290-128_B_F_1773176088fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag01/30/1210/28/16137Genomicunknown
ss481930612ILLUMINA|HumanOmniExpress-12v1_C_rs9424290-131_B_F_1857973205fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag01/30/1210/27/16137Genomicunknown
ss482888116ILLUMINA|HumanOmni1-Quad_v1-0_C_rs9424290-131_B_F_1865476553fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag01/30/1208/28/15146Genomicunknown
ss485742755ILLUMINA|HumanOmni2.5-4v1_D_rs9424290-131_B_F_1857973205fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag01/30/1210/27/16137Genomicunknown
ss537597638ILLUMINA|HumanOmni5-4v1_B_rs9424290-131_B_F_1891394431fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag06/22/1208/28/15146Genomicunknown
ss553734758TISHKOFF|snp_chr1_3742009fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag11/22/1211/22/12138Genomicunknown
ss647536570SSMP|1_3742009fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag12/14/1202/09/15138Genomicunknown
ss778638790ILLUMINA|HumanOmni25Exome-8v1_A_rs9424290-131_B_F_1865476553fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag05/30/1307/09/15146Genomicunknown
ss783317153ILLUMINA|HumanOmni2.5-4v1_H_rs9424290-131_B_F_1857973205fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag05/30/1307/28/15146Genomicunknown
ss784269146ILLUMINA|HumanOmniExpressExome-8v1_A_rs9424290-131_B_F_1891394431fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag05/31/1306/18/15146Genomicunknown
ss832578692ILLUMINA|HumanOmniExpress-12v1_H_rs9424290-131_B_F_1857973205fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag09/17/1306/18/15146Genomicunknown
ss834096470ILLUMINA|HumanOmni2.5-8v1_A_rs9424290-131_B_F_1865476553fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag09/18/1307/28/15146Genomicunknown
ss974796597EVA-GONL|EVA-GONL_rs9424290fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag04/23/1404/23/14142Genomicunknown
ss1067627392JMKIDD_LAB|HGDP_WGS_chr1_3742009fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag07/10/1407/10/14142Genomicunknown
ss12894521311000GENOMES|PHASE3_V1_120880fwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag08/16/1408/16/14142Genomicunknown
ss1397238568HAMMER_LAB|HAMMER_LAB_rs9424290fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag09/30/1409/30/14146Genomicunknown
ss1573860193EVA_GENOME_DK|EVA_GENOME_DK_snv_rs9424290fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag02/19/1502/19/15144Genomicunknown
ss1584155360EVA_DECODE|EVA_DECODE_1_3731869_26099_rs9424290fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag03/02/1503/02/15144Genomicunknown
ss1599427621EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_3742009_53877fwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag03/04/1503/04/15144Genomicunknown
ss1642421654EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_3742009_53877fwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag03/04/1503/04/15144Genomicunknown
ss1751917919ILLUMINA|OmniExpressExome-8v1-1_B_rs9424290-131_B_F_1891394431fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag05/27/1506/09/15146Genomicunknown
ss1917992128WEILL_CORNELL_DGM|SNV:chr1:3742009fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag10/16/1510/16/15147Genomicunknown
ss1966671411GENOMED|rs9424290fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag02/16/1602/16/16147Genomicunknown
ss2019512227JJLAB|SNP14782fwd/BC/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag08/29/1608/30/16149Genomicunknown
ss2147502594USC_VALOUEV|NC_000001.10:g.3742009C>Tfwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag11/17/1611/17/16150Genomicunknown
ss2159575545HUMAN_LONGEVITY|HLI-1-3825445-C-Tfwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag11/18/1611/18/16150Genomicunknown
ss2624271880SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV9184fwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag01/06/1701/06/17151Genomicunknown
ss2632468702ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs9424290-131_B_F_18913944fwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag02/02/1702/02/17151Genomicunknown
ss2697396643GRF|rs9424290fwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag02/13/1702/13/17151Genomicunknown
ss2750973498GNOMAD|rs9424290fwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag05/17/1705/17/17151Genomicunknown
ss2986201524SWEGEN|NC_000001.10:g.3742009C>Tfwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag05/30/1705/30/17151Genomicunknown
ss3023519731BIOINF_KMB_FNS_UNIBA|1.3825445C>Tfwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag07/05/1707/05/17151Genomicunknown
ss3343289024CSHL|rs9424290fwd/C/Tctataaagcaagaaatccaacatgagccacatggttccgtttctacaaag10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9424290|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GGCAGTGGCA CTGTGGGAAG GGGGACAGTG GCACTGTGGG AAGGGGGCAG TGGCACTGTG
 GGAAGGGGGC AGTGGCACTG TGGGAAGGGG GGCAGTGGCA CTGTGGGAAG GGGGCAGTGG
 CACTGTGGGA AGGGAGCAGT GGCACTGTGG GAAGGGGGGC AGTGGCACTG TGGGAAGGGG
 GCAGTGGCAC TGTGGGAAGG GGGCAGTGGC ACTGTGGGAA GGGGGCAGTG CCTGTGCTGC
 TGGCAGTGGT GCCCAGGCAC AACCCCTTTG GAGCACTCCT GGGCAGCCCC ACTGAGCATC
 AGCACACCTG GCAATCCCAC AACACATTGT GAACCCAAGA AAGTGCATTC CTGTGCATCC
 TGGAAGACAC CAGAACGCTG TGGCAACATT GTTTATCATG GTCCCAAACT GGACGCAGCC
 CTGGCGCACA GCGGAAGGTG GATGAAGGTG CTGTGGTCCA TTCAAGCAGT GGACACTATA
 AAGCAAGAAA TCCAACATGA
 Y
 GCCACATGGT TCCGTTTCTA CAAAGCTCAA AGAGCAAGGA GGACCCATTT GTGGTGTCAG
 AAATCAGACC CCTGCTGACT CTGGAAGGAG CCCCGAGGGG AGGTGGCGGC ACAGCATGTT
 TCCGGTTCAC TGGGCTGTCT GTCATATGGA ATGACTCGCA CGCATTTGCG GGTGTGTGCT
 TGGCTTCAGT TACTTTTCTC GCAACCTCTC CTCTGAAAAT ACTAAGACTT GGGACAGCTT
 TTTGACTCGG CCTTTCAACA GCCAGGTGTT CCCGCTCATG CAAGTAGCTG GCTGCTGTGC
 CGCTGGCCTG ACCTGTTTGC AGTGGTCACA TCTTGTCAGC ATGAGACAGT GCTTCCAGTA
 GTGGAGATCC AGACCTTCCT CTGTGAAGGA TTCACTCCTT TCCCCACAAA AAATACACAA
 ACTGAAAGCA AAGCAAAGCA GGAAATAAAG GTAAGGATCT AGTTCCACTG ATGGCCGTTC
 CGCTCCCACG TCACGAGGAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_004321
dbSNP Blast Analysis

  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
ss1289452131EAS 1008AF 0.392900020.60710001
EUR 1006AF 0.940400000.05960000
AFR 1322AF 0.967500030.03250000
AMR 694AF 0.842899980.15709999
SAS 978AF 0.706499990.29350001
ss12992583HapMap-CEUEuropean 114IG0.859649120.122807020.017543860.250592000.921052630.07894737
HapMap-HCBAsian 90IG0.133333340.377777790.488888890.371093000.322222230.67777777
HapMap-JPTAsian 90IG0.155555560.533333360.311111120.583882000.422222230.57777780
HapMap-YRISub-Saharan African 120IG0.949999990.05000000 1.000000000.975000020.02500000
ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss218203328pilot_1_YRI_low_coverage_panel 118AF 0.974576290.02542373
ss230404207pilot_1_CEU_low_coverage_panel 120AF 0.941666660.05833333
ss238123086pilot_1_CHB+JPT_low_coverage_panel 120AF 0.391666680.60833335
ss68756691HapMap-CEUEuropean 120IG0.883333330.100000000.016666670.150222000.933333340.06666667
HapMap-HCBAsian 90IG0.133333340.377777790.488888890.371093000.322222230.67777777
HapMap-JPTAsian 90IG0.155555560.533333360.311111120.583882000.422222230.57777780
HapMap-YRISub-Saharan African 120IG0.966666640.03333334 1.000000000.983333350.01666667

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.345+/-0.2310000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN