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Reference SNP (refSNP) Cluster Report: rs139428292                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:134/150
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G/T (REV)
Allele Origin:G:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:A=0.0237/1958 (ExAC)
A=0.0096/48 (1000 Genomes)
A=0.0212/276 (GO-ESP)
HGVS Names
  • NC_000001.10:g.145507646G>A
  • NC_000001.11:g.145927447C>A
  • NC_000001.11:g.145927447C>T
  • NG_032654.2:g.5090G>A
  • NG_032654.2:g.5090G>T
  • NM_005105.4:c.-21G>A
  • NM_005105.4:c.-21G>T
  • NW_003871055.3:g.2742860C>T
  • XM_005272985.1:c.-21G>A
  • XM_005277456.1:c.-21G>A
  • XM_005277457.1:c.-326G>A
  • XM_005277458.1:c.-266G>A
  • XR_001737729.1:n.364C>A
  • XR_001737729.1:n.364C>T
  • XR_001737730.1:n.-116C>A
  • XR_001737730.1:n.-116C>T
  • XR_001737731.1:n.-116C>A
  • XR_001737731.1:n.-116C>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 ss253467047 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs139428292 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
ss253467047BL|SNP133459_1_144219003fwd/TA/Gcgaggtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggcggacg08/18/1008/18/10134Genomicunknown
ss3289164481000GENOMES|20100804_snps_559984_chr1_145507646fwd/A/Gcgaggtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggcggacg03/22/1103/22/11134Genomicunknown
ss4897609911000GENOMES|20110521_exome_314364_chr1_145507646fwd/TA/Gcgaggtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggcggacg02/10/1202/21/12137Genomicunknown
ss491602072CLINSEQ_SNP|SNV-chr1-144219003byFreqfwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc03/06/1209/05/14137Genomicunknown
ss648379162SSMP|1_145507646fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc12/14/1202/09/15138Genomicunknown
ss712338592NHLBI-ESP|ESP6500SI-chr1-145507646fwd/TA/Gcgaggtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggcggacg02/20/1302/20/13138Genomicunknown
ss975638413EVA-GONL|EVA-GONL_rs139428292fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc04/23/1404/23/14144Genomicunknown
ss1026803189F_HASHEMI|NG_032654.1:g.5090G>Afwd/TA/Gcgaggtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggcggacg06/06/1406/06/14141Genomicunknown
ss12927334711000GENOMES|PHASE3_V1_3536173fwd/A/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc08/16/1408/16/14142Genomicunknown
ss1574366507EVA_GENOME_DK|EVA_GENOME_DK_snv_rs139428292fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc02/19/1502/19/15144Genomicunknown
ss1584010574EVA_FINRISK|EVA_FINRISK_rs139428292fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc02/27/1502/27/15144Genomicunknown
ss1585020384EVA_DECODE|EVA_DECODE_1_144219003_891136_rs139428292fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc03/02/1503/02/15144Genomicunknown
ss1601125507EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_145507646_1922601fwd/A/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc03/04/1503/04/15144Genomicunknown
ss1644119540EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_145507646_1922601fwd/A/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc03/04/1503/04/15144Genomicunknown
ss1685735706EVA_EXAC|EVA_EXAC_558520fwd/A/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc03/04/1503/04/15144Genomicunknown
ss1685735707EVA_EXAC|EVA_EXAC_558521fwd/G/Ttacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc03/04/1503/04/15144Genomicunknown
ss1710920784EVA_MGP|EVA_XIMO_37536fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc03/09/1503/09/15144Genomicunknown
ss1918860799WEILL_CORNELL_DGM|SNV:chr1:145507646fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc10/16/1510/16/15147Genomicunknown
ss1958311327ILLUMINA|1:145507646-G-A-0_T_F_2304257551fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc11/13/1511/13/15147Genomicunknown
ss2019949767JJLAB|SNP452322fwd/TA/Gtacctagtgtctgagcggcacagacagatctcgatcgaaggcgagatggc08/29/1608/30/16149Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs139428292|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G/T'|mol=Genomic|build=149
 CCGCGGTTAA GAGGAAGCCA CGGCCCCCTG TAGTCTGTAC CTCCTAAGAT GGATGATTTA
 GCTTGCGATC TGTTCAAGAT GGCCACAGAA ACACTTCCGG TATCTTTCCG CACTAGGCCC
 GCCCCAATTT GCGTGTTTTT ACCGTGCAGA GGGAGGGATT TAGAGTTAGC CTTTGATTGG
 TCAGCTTGAC TGGCGACCTT TCCCCTCTGC GACAGTTTCC CGAGGTACCT AGTGTCTGAG
 CGGCACAGAC
 D
 AGATCTCGAT CGAAGGCGAG ATGGCGGACG TGCTAGATCT TCACGAGGCT GGGGGCGAAG
 ATTTCGCCAT GGATGAGGAT GGGGACGGTG AGGACAGTGG AGACGGCTGG TGGGAAGCGG
 GGAAGGTGCG AGAGAAGGCT ATAATAGGAA AATTTACTCT TTTTTCCTCG GTCGTAAGGA
 TGGGAATCGA GGAACCGGGT CTTGGGTGGA TTAGAGATTC CGCCCCCTTC AGGAGAAGGG
 AGGGCGTGAC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
OMIM
605313

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs139428292 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/G
G/G
HWPA
G
T
ss1292733471EAS 1008AF 1.00000000
EUR 1006AF 0.031800000.96820003
AFR 1322AF 0.000800000.99919999
AMR 694AF 0.015900000.98409998
SAS 978AF 0.004100000.99589998
ss1685735706ExAc_Aggregated_Populations121389AF 0.017761080.98223889
ss1685735707ExAc_Aggregated_Populations119234AF 0.999991600.00000839
ss491602072CSAgilent 673GF0.042000000.958000001.000000000.021000000.97899997

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.046+/-0.1450000

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

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