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Reference SNP (refSNP) Cluster Report: rs12021500                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
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:C=0.2873/1439 (1000 Genomes)
C=0.2540/31895 (TOPMED)
HGVS Names
  • CM000663.2:g.113524369T>C
  • NC_000001.10:g.114066991T>C
  • NC_000001.11:g.113524369T>C
  • NM_001142782.1:c.317-25146T>C
  • NM_152900.2:c.317-25146T>C
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 ss18069701 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12021500 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
ss18069701SC_SNP|SC-CHR1_NA11321-200402.chr1.NT_019273.16_5062939fwd/BC/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca02/20/0403/04/04120Genomicunknown
ss1085366591000GENOMES|CEU.trio.12.15.2008_147067_chr1_113868514fwd/BC/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca12/16/0812/16/08130Genomicunknown
ss165056795COMPLETE_GENOMICS|NA07022_36_chr1_113868514fwd/BC/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca09/28/0909/30/09132Genomicunknown
ss167017590COMPLETE_GENOMICS|NA20431_36_chr1_113868514fwd/BC/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca09/30/0909/30/09132Genomicunknown
ss198953760BUSHMAN|BUSHMAN-chr1-113868513fwd/BC/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca02/16/1003/06/10132Genomicunknown
ss2186057931000GENOMES|pilot_1_YRI_415476_chr1_113868514fwd/C/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca04/22/1004/22/10132Genomicunknown
ss2306982001000GENOMES|pilot_1_CEU_302829_chr1_113868514fwd/C/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca05/01/1005/01/10132Genomicunknown
ss2383546071000GENOMES|pilot_1_CHB+JPT_239684_chr1_113868514fwd/C/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca05/01/1005/01/10132Genomicunknown
ss253396225BL|SNP119031_1_113868514fwd/BC/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca08/18/1008/18/10134Genomicunknown
ss275984231GMI|GMI_AK_SNP_304394fwd/C/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca12/16/1012/16/10137Genomicunknown
ss284124090GMI|GMI_NA10851_SNP_136856fwd/C/Tagatccacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatgaaaaca12/17/1012/17/10138Genomicunknown
ss554593849TISHKOFF|snp_chr1_114066991fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga11/22/1211/22/12138Genomicunknown
ss648323194SSMP|1_114066991fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga12/14/1202/09/15138Genomicunknown
ss975586727EVA-GONL|EVA-GONL_rs12021500fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga04/23/1404/23/14142Genomicunknown
ss1068205078JMKIDD_LAB|HGDP_WGS_chr1_114066991fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga07/10/1407/10/14142Genomicunknown
ss12924951581000GENOMES|PHASE3_V1_3289655fwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga08/16/1408/16/14142Genomicunknown
ss1425942102DDI|DDI_rs12021500fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga11/04/1411/04/14144Genomicunknown
ss1574333497EVA_GENOME_DK|EVA_GENOME_DK_snv_rs12021500fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga02/19/1502/19/15144Genomicunknown
ss1584967572EVA_DECODE|EVA_DECODE_1_113868514_838324_rs12021500fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga03/02/1503/02/15144Genomicunknown
ss1601023722EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_114066991_1810945fwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga03/04/1503/04/15144Genomicunknown
ss1644017755EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_114066991_1810945fwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga03/04/1503/04/15144Genomicunknown
ss1794956518HAMMER_LAB|Hsieh_350309fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga07/15/1507/15/15146Genomicunknown
ss1918787047WEILL_CORNELL_DGM|SNV:chr1:114066991fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga10/16/1510/16/15147Genomicunknown
ss1966845206GENOMED|rs12021500fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga02/16/1602/16/16147Genomicunknown
ss2019917959JJLAB|SNP420514fwd/BC/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga08/29/1608/30/16149Genomicunknown
ss2147936668USC_VALOUEV|NC_000001.10:g.114066991T>Cfwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga11/17/1611/17/16150Genomicunknown
ss2165842494HUMAN_LONGEVITY|HLI-1-113524369-T-Cfwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga11/18/1611/18/16150Genomicunknown
ss2624468612SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV265501fwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga01/06/1701/06/17151Genomicunknown
ss2697866989GRF|rs12021500fwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga02/13/1702/13/17151Genomicunknown
ss2759738793GNOMAD|rs12021500fwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga05/17/1705/17/17151Genomicunknown
ss2987464374SWEGEN|NC_000001.10:g.114066991T>Cfwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga05/30/1705/30/17151Genomicunknown
ss3023723482BIOINF_KMB_FNS_UNIBA|1.113524369T>Cfwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga07/05/1707/05/17151Genomicunknown
ss3343642459CSHL|rs12021500fwd/C/Tcacagacagcttgcaccagaaaagcgcagacactcaacaccagcccatga10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12021500|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 cagagaccat tgcggcagcc ccttccatca caggcctgga gaccgaggag gaaaaaattg
 ttcagtgggc tgggccggga tccctctgct gtgtgcagtc tagggacttg gtgccctgtg
 tcccagccac tccagctgtg actaaaaggg gccaaggtac agctcgggcc atggcttcag
 aggttgcagg ccctaagctc tggcagtttc catgtggtgt tgagcctgca ggtgcataga
 agtcaagaat tgagatttgg aaacctctgc ctagatttca gaggatttat ggaaatgctt
 ggatgtccag gcagaagttt gctgcgggga tggggcactc atggagaacc tttgctaagg
 cagtgccaaa gcaaaatgtg gggtgggtat gcccacagag agtccccact ggggtgctgc
 ctcgtggaga tgtgagaaga gggccaccat cctccagacc ccagaatggt agatccacag
 acagcttgca ccagaaaagc
 Y
 gcagacactc aacaccagcc catgaaaaca gccaggaagg aggctgtacc ctgcaaagcc
 acagggacag agctgcccaa gaccatggga acccacctct ggcatcagca tgacctggat
 gtgagacatg gagtctaagg ggataatttt ggagctttaa gatttgactg ccctactaga
 tttcggactt gcatggggtc tttagcccct ttgtttagcc aatttctccc atttggaatg
 ggtgtattta tccaatgcct gtatccccat tgtgtctagg aagttactaa cttgcttttg
 attttgcagg ctcataggca gaagggactt gccttgtctc agttgagaca tttgactgaa
 cttttgagtt aatgctgaaa tgagttaaga ctttggggaa ctgttagaag acatgattgg
 ttttgaaatg tgaagagatg agatttggga gggaccctgg gcagaatgat atggtttggc
 tgtgttccca cccaaatctc

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_019273
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/T
HWPC
T
ss1292495158EAS 1008AF 0.609099980.39089999
EUR 1006AF 0.235599990.76440001
AFR 1322AF 0.144500000.85549998
AMR 694AF 0.332899990.66710001
SAS 978AF 0.169700000.83029997
ss165056795CEUEuropean 2IG1.00000000 0.500000000.50000000
ss167017590PGP 2IG1.00000000 0.500000000.50000000
ss218605793pilot_1_YRI_low_coverage_panel 118AF 0.152542370.84745765
ss230698200pilot_1_CEU_low_coverage_panel 120AF 0.216666670.78333336
ss238354607pilot_1_CHB+JPT_low_coverage_panel 120AF 0.566666660.43333334

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.410+/-0.1920000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN