NCBI
dbSNP
Attention: This page will be retired!
This legacy RefSNP page contains old data from dbSNP build 151 (March 2018) and is no longer maintained.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.
Spacer gif

Spacer gif
Reference SNP (refSNP) Cluster Report: rs9424288                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.3097/1551 (1000 Genomes)
A=0.3328/41788 (TOPMED)
HGVS Names
  • CM000663.2:g.3821175A>C
  • NC_000001.10:g.3737739A>C
  • NC_000001.11:g.3821175A>C
  • NG_046726.1:g.41059T>G
  • NM_014704.3:c.2571+1999T>G
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 ss12992579 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9424288 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
ss12992579SC_SNP|NT_004321.15_1044513byFreqfwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct10/22/0310/25/06119Genomicunknown
ss16419195CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_004321.15_1044513fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct02/17/0403/04/04120Genomicunknown
ss20574231SSAHASNP|WGSA-200403-chr1.chr1.NT_004321.15_1044513fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct03/18/0403/18/04121Genomicunknown
ss41217177ABI|hCV26892400fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct07/16/0507/17/05126Genomicunknown
ss77565925HGSV|Cor12156_SNV_20070510.chr1_3760896fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct10/09/0710/13/07129Genomicunknown
ss85667026HGSV|Cor18517_SNV_20070510.chr1_3760896fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct12/06/0712/09/07130Genomicunknown
ss87174444BCMHGSC_JDW|JWB-0002820fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct02/26/0802/26/08129Genomicunknown
ss97915497HUMANGENOME_JCVI|1103675006487fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct03/30/0803/30/08130Genomicunknown
ss105114947BGI|BGI_rs9424288fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct08/06/0806/16/09131Genomicunknown
ss1079490731000GENOMES|CEU.trio.12.15.2008_3332_chr1_3727599fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct12/15/0812/15/08130Genomicunknown
ss1099675681000GENOMES|NA19240_2008_12_16_3750_chr1_3727599fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct12/17/0812/17/08130Genomicunknown
ss118453555ILLUMINA-UK|NA18507_000003505_NCBI36.1_chr1_3727599fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct01/21/0901/21/09130Genomic99 %
ss138971434ENSEMBL|ENSSNP215320fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct12/08/0810/16/09131Genomicunknown
ss163004935COMPLETE_GENOMICS|NA19240_36_chr1_3727599fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct09/29/0909/29/09132Genomicunknown
ss163738273COMPLETE_GENOMICS|NA07022_36_chr1_3727599fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct09/28/0909/29/09132Genomicunknown
ss197925145BUSHMAN|BUSHMAN-chr1-3727598fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct02/16/1003/05/10132Genomicunknown
ss205344357BCM-HGSC-SUB|BCM_CMT_1011-151693fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct03/15/1003/15/10132Genomicunknown
ss2182032931000GENOMES|pilot_1_YRI_12976_chr1_3727599fwd/A/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct04/22/1004/22/10132Genomicunknown
ss2304041811000GENOMES|pilot_1_CEU_8810_chr1_3727599fwd/A/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct05/01/1005/01/10132Genomicunknown
ss2381230591000GENOMES|pilot_1_CHB+JPT_8136_chr1_3727599fwd/A/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct05/01/1005/01/10132Genomicunknown
ss252880463BL|SNP4519_1_3727599fwd/TA/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct08/18/1008/18/10134Genomicunknown
ss275691479GMI|GMI_AK_SNP_11640fwd/A/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct12/16/1012/16/10137Genomicunknown
ss283991025GMI|GMI_NA10851_SNP_3791fwd/A/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct12/17/1012/17/10138Genomicunknown
ss290498334PJP|SNP_4692_chr1_3727599fwd/A/Cgtgcccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagctctct01/21/1101/21/11134Genomicunknown
ss553734729TISHKOFF|snp_chr1_3737739fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc11/22/1211/22/12138Genomicunknown
ss647536528SSMP|1_3737739fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc12/14/1202/09/15138Genomicunknown
ss974796542EVA-GONL|EVA-GONL_rs9424288fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc04/23/1404/23/14142Genomicunknown
ss1067627354JMKIDD_LAB|HGDP_WGS_chr1_3737739fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc07/10/1407/10/14142Genomicunknown
ss12894519701000GENOMES|PHASE3_V1_120715fwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc08/16/1408/16/14142Genomicunknown
ss1425693037DDI|DDI_rs9424288fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc11/04/1411/04/14144Genomicunknown
ss1573860169EVA_GENOME_DK|EVA_GENOME_DK_snv_rs9424288fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc02/19/1502/19/15144Genomicunknown
ss1584155313EVA_DECODE|EVA_DECODE_1_3727599_26052_rs9424288fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc03/02/1503/02/15144Genomicunknown
ss1599427520EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_3737739_53768fwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc03/04/1503/04/15144Genomicunknown
ss1642421553EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_3737739_53768fwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc03/04/1503/04/15144Genomicunknown
ss1793785169HAMMER_LAB|Hsieh_12173fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc07/15/1507/15/15146Genomicunknown
ss1917992069WEILL_CORNELL_DGM|SNV:chr1:3737739fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc10/16/1510/16/15147Genomicunknown
ss1966671398GENOMED|rs9424288fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc02/16/1602/16/16147Genomicunknown
ss2019512189JJLAB|SNP14744fwd/TA/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc08/29/1608/30/16149Genomicunknown
ss2147502565USC_VALOUEV|NC_000001.10:g.3737739A>Cfwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc11/17/1611/17/16150Genomicunknown
ss2159575241HUMAN_LONGEVITY|HLI-1-3821175-A-Cfwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc11/18/1611/18/16150Genomicunknown
ss2624271857SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV9161fwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc01/06/1701/06/17151Genomicunknown
ss2697396607GRF|rs9424288fwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc02/13/1702/13/17151Genomicunknown
ss2750973121GNOMAD|rs9424288fwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc05/17/1705/17/17151Genomicunknown
ss2986201442SWEGEN|NC_000001.10:g.3737739A>Cfwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc05/30/1705/30/17151Genomicunknown
ss3023519717BIOINF_KMB_FNS_UNIBA|1.3821175A>Cfwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc07/05/1707/05/17151Genomicunknown
ss3343288989CSHL|rs9424288fwd/A/Ccagatggctgattccaggtccggggaggaaggcaccaaacaggagggagc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9424288|allelePos=251|totalLen=1057|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=151
 AGGAGACACA GATGTTGGGA GAGACAAGGT TAAATAAAGC CTGCAGCTCA GAACGGGAAG
 GGGAAGTGTG TGTGCATGAG TGATGGAGCT TACTTCCCTT Gatttctcct ggctgtgtcc
 actgagagtc cagccacagc gaactaccca gcagcagtgg gcatgaggcc cccagcgctg
 tcctgagaca tccattcctg ctaatgggaa ccaggcctct gtgcccagat ggctgattcc
 aggtccgggg
 M
 aggaaggcac caaacaggag ggagctctct gaggctgcgt ggctctcatc caggcctcag
 gagcccagct gaagagtctg ccataggcta gagctgggat aattcacgca tcactaagca
 tggtaactgc tgtgactgga acacattgaa taatttaaat ccatggttca taacgacact
 acagacaaaa caaaacaaat tagctgccat ggaagatgct agtgacccag cttactattc
 tgaaaaccag taaaccaagg aaaaaaatta aaccttcact ctgcctttcc aatagaaagt
 ctaacctagg gtcaccacag agtggacgag cttctgctta gaggaatatc ccagcagatg
 aacgaaggag ggatgacaga atgaggcccc tcctgagtcg gtgggttagg ccttgagcct
 cagcagctgc caccgtcaca catatcacgc gcctcccggg ggacacacca gcattgcctg
 tgaagcggcc acactcacac cgagcctgtg cacacctgat gaggcccaga gatcccacct
 cctgtttaca ggaaatacag ggacagagaa acaggttaag cgcccccaag ggaacgtagt
 cagcagatcc agacgatgag aagccctacg gggcaaacag ctccttcctt caccaagtga
 atcataagga aaaagaacga gagaatgaac ctgttcaaaa cagacCAACC AGGCACCGGG
 GCCTTCTATG GATCCCGGTA ATCAGATGCT TCTGACCTGA TGAGATGGCG GCAATGTGAC
 TGACGTCTGG AAGGCTGAGG CTGCTG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_004321 ABBA01073650
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.
SourceA/A
A/C
C/C
HWPA
C
ss118453555YRI 2IG 1.00000000 0.500000000.50000000
ss1289451970EAS 1008AF 0.338300020.66170001
EUR 1006AF 0.429400000.57060003
AFR 1322AF 0.084700000.91530001
AMR 694AF 0.491399970.50860000
SAS 978AF 0.332300010.66769999
ss12992579HapMap-CEUEuropean 114IG0.210526320.456140340.333333340.583882000.438596490.56140351
HapMap-HCBAsian 88IG0.090909090.386363630.522727250.751830000.284090910.71590906
HapMap-JPTAsian 90IG0.155555560.488888890.355555561.000000000.400000010.60000002
HapMap-YRISub-Saharan African 116IG 0.051724140.948275861.000000000.025862070.97413790
ss138971434ENSEMBL_Venter 2IG 1.00000000 1.00000000
ENSEMBL_celera 4IG 1.00000000 1.00000000
ss163004935YRISub-Saharan African 2IG 1.00000000 1.00000000
ss163738273CEUEuropean 2IG 1.00000000 1.00000000
ss218203293pilot_1_YRI_low_coverage_panel 118AF 0.050847460.94915253
ss230404181pilot_1_CEU_low_coverage_panel 120AF 0.466666670.53333336
ss238123059pilot_1_CHB+JPT_low_coverage_panel 120AF 0.358333320.64166665
ss97915497J. Craig Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.428+/-0.1760000

  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_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN