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Reference SNP (refSNP) Cluster Report: rs12144939                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G/T (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.2378/1191 (1000 Genomes)
T=0.2335/29314 (TOPMED)
HGVS Names
  • CM000663.2:g.196729815G>A
  • CM000663.2:g.196729815G>T
  • NC_000001.10:g.196698945G>T
  • NC_000001.11:g.196729815G>A
  • NC_000001.11:g.196729815G>T
  • NG_007259.1:g.82805G>A
  • NG_007259.1:g.82805G>T
  • NM_000186.3:c.2413+1293G>A
  • NM_000186.3:c.2413+1293G>T
  • XR_001737134.1:n.2636+1293G>A
  • XR_001737134.1:n.2636+1293G>T
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 ss18296289 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12144939 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
ss18296289SC_SNP|SC-CHR1_NA07340-200402.chr1.NT_004671.15_8053931byFreqfwd/BG/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt02/20/0410/26/06120Genomicunknown
ss20582686SSAHASNP|WGSA-200403-chr1.chr1.NT_004671.15_8053931fwd/BG/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt03/18/0403/18/04121Genomicunknown
ss39692513ABI|hCV11890118fwd/BG/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt07/16/0507/17/05126Genomicunknown
ss48532189PGA-UW-FHCRC|CFH-079749byFreqfwd/A/G/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt10/13/0511/03/06126Genomicunknown
ss119164558ILLUMINA-UK|NA18507_000201797_NCBI36.1_chr1_194965568fwd/BG/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt01/21/0901/22/09131Genomic99 %
ss139109318ENSEMBL|ENSSNP126244fwd/BG/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt12/08/0810/16/09131Genomicunknown
ss199446476BUSHMAN|BUSHMAN-chr1-194965567fwd/BG/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt02/16/1003/06/10132Genomicunknown
ss2107084631000GENOMES|YRI.trio.3.2010_88489_chr1_194965568fwd/BG/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt03/29/1003/29/10132Genomicunknown
ss2188099581000GENOMES|pilot_1_YRI_619641_chr1_194965568fwd/G/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt04/22/1004/22/10132Genomicunknown
ss2308477991000GENOMES|pilot_1_CEU_452428_chr1_194965568fwd/G/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt05/01/1005/01/10132Genomicunknown
ss2384703471000GENOMES|pilot_1_CHB+JPT_355424_chr1_194965568fwd/G/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt05/01/1005/01/10132Genomicunknown
ss284204647GMI|GMI_NA10851_SNP_217413fwd/G/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt12/17/1012/17/10138Genomicunknown
ss290697474PJP|SNP_203832_chr1_194965568fwd/G/Tagattttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatccattt01/21/1101/21/11134Genomicunknown
ss555016395TISHKOFF|snp_chr1_196698945fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc11/22/1211/23/12138Genomicunknown
ss648607029SSMP|1_196698945fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc12/14/1202/09/15138Genomicunknown
ss1068496455JMKIDD_LAB|HGDP_WGS_chr1_196698945fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc07/10/1407/10/14142Genomicunknown
ss12940990241000GENOMES|PHASE3_V1_4958105fwd/A/Gttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc08/16/1408/16/14142Genomicunknown
ss12940990251000GENOMES|PHASE3_V1_4958106fwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc08/16/1408/16/14142Genomicunknown
ss1426070139DDI|DDI_rs12144939fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc11/04/1411/04/14144Genomicunknown
ss1574589635EVA_GENOME_DK|EVA_GENOME_DK_snv_rs12144939fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc02/19/1502/19/15144Genomicunknown
ss1585390966EVA_DECODE|EVA_DECODE_1_194965568_1261723_rs12144939fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc03/02/1503/02/15144Genomicunknown
ss1601841387EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_196698945_2710138fwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc03/04/1503/04/15144Genomicunknown
ss1601841388EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_196698945_2710139fwd/A/Gttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc03/04/1503/04/15144Genomicunknown
ss1644835420EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_196698945_2710138fwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc03/04/1503/04/15144Genomicunknown
ss1644835421EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_196698945_2710139fwd/A/Gttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc03/04/1503/04/15144Genomicunknown
ss1795525794HAMMER_LAB|Hsieh_521051fwd/TA/Gttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc07/15/1507/15/15146Genomicunknown
ss1919226954WEILL_CORNELL_DGM|SNV:chr1:196698945fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc10/16/1510/16/15147Genomicunknown
ss1966938972GENOMED|rs12144939fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc02/16/1602/16/16147Genomicunknown
ss2020132179JJLAB|SNP634734fwd/BG/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc08/29/1608/30/16149Genomicunknown
ss2148159223USC_VALOUEV|NC_000001.10:g.196698945G>Tfwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc11/17/1611/17/16150Genomicunknown
ss2168972866HUMAN_LONGEVITY|HLI-1-196729815-G-A,Tfwd/A/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc11/18/1611/18/16150Genomicunknown
ss2698147184GRF|rs12144939fwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc02/13/1702/13/17151Genomicunknown
ss2764656619GNOMAD|rs12144939fwd/A/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc05/17/1705/17/17151Genomicunknown
ss2988223006SWEGEN|NC_000001.10:g.196698945G>Tfwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc05/30/1705/30/17151Genomicunknown
ss3023826021BIOINF_KMB_FNS_UNIBA|1.196729815G>Tfwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc07/05/1707/05/17151Genomicunknown
ss3099814457TOPMED|TOPMed_freeze_5?chr1:196,729,815-01fwd/A/Gttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc09/28/1709/28/17151Genomicunknown
ss3099814458TOPMED|TOPMed_freeze_5?chr1:196,729,815-02fwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc09/28/1709/28/17151Genomicunknown
ss3343847743CSHL|rs12144939fwd/G/Tttctatttcctctgaattaatcgtctaggctgtgtgtctagaaatttatc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12144939|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G/T'|mol=Genomic|build=151
 TAGTTTTAGC CATTCTATAT AGatttatta aaatgatcgt atagttatcg tcctttctgt
 taatgggatg catcaccttt actaatttgc ctatgttaaa cgacctttac atttcttgga
 ttaaacccat ttgatcatag tgaatgatct ttttaatgtg ctgtaggatt tgttttccta
 gtatagtgtt gaggggtttt gtacctatgt tcatcagggg attttgcctg tagttttctt
 tttgcgttgt gtccttgtct ggttttggtt ccagagtaat gttgggccac tagaatgagt
 tagaaaaatg atctcctcat caaatttttg gagtcgtttt agaagaattg gtattagtcc
 tttctaaaat gttgttataa ttcagcaatg aagccatcag gtcttggatt ttctttgatg
 ggaaacattt tattactgac ttaatctgtt gcctcatgat tactctgttc agattttcta
 tttcctctga attaatcgtc
 D
 taggctgtgt gtctagaaat ttatccattt cttctaggtt atccaatttg ttggcatata
 attgctaata acggtctctc attatacttt gtattttttt gatatcagtt gtaatatcac
 ccttttcatc tccgatcttg tgtttcttta agccgtatct ctctttttta gttattctgg
 ttaaagcttt gtcaattttt gattatctaa aaaaaaacta ttttcattga tattttgtac
 tgctttgggg gctctatttt acttactttt actctgatct ttatgatttc catccttcta
 ctaattttgg aattgactag tttgttcatg tttttctgct tctttgaggt gtactactag
 actgtttatt tgagttcttt ccactttctt gatataggca attattccta aaaacatcca
 tcttagaact acttttgctg catcccataa gttttgctac gttttgtttc cattctcctt
 tactgaaaat atttttaaat

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_004671
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/G
A/T
G/G
G/T
T/T
HWPA
G
T
ss119164558YRI 2IG 1.00000000 1.00000000
ss139109318ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss18296289HapMap-CEUEuropean 112IG 0.625000000.321428570.053571430.75183000 0.785714270.21428572
HapMap-HCBAsian 90IG 0.822222230.17777778 1.00000000 0.911111120.08888889
HapMap-JPTAsian 90IG 0.888888900.11111111 1.00000000 0.944444420.05555556
HapMap-YRISub-Saharan African 114IG 0.280701760.491228070.228070171.00000000 0.526315810.47368422
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss199446476BANTU 2IG 1.00000000 0.500000000.50000000
ss218809958pilot_1_YRI_low_coverage_panel 118AF 0.550847470.44915253
ss230847799pilot_1_CEU_low_coverage_panel 120AF 0.766666650.23333333
ss238470347pilot_1_CHB+JPT_low_coverage_panel 120AF 0.925000010.07500000
ss48532189PGA_CEPH-PANELEuropean 44IG 0.500000000.363636370.136363640.47950000 0.681818190.31818181
PGA_YORUB-PANELSub-Saharan African 40IG0.050000000.050000000.250000000.300000010.349999990.406570000.050000000.425000010.52499998

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.400+/-0.2310000

  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
UNKNOWNUNKNOWNYES

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