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dbSNP
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Reference SNP (refSNP) Cluster Report: rs56298562                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:129/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:C:germline
T:germline
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:A=0.0231/2770 (ExAC)
A=0.0134/67 (1000 Genomes)
A=0.0177/230 (GO-ESP)
A=0.0153/1925 (TOPMED)
HGVS Names
  • CM000670.2:g.27463119G>A
  • NC_000008.10:g.27320636G>A
  • NC_000008.11:g.27463119G>A
  • NG_015827.1:g.21178C>T
  • NM_000742.3:c.1324C>T
  • NM_001282455.1:c.1279C>T
  • NM_001347705.1:c.847C>T
  • NM_001347706.1:c.847C>T
  • NM_001347707.1:c.730C>T
  • NM_001347708.1:c.730C>T
  • NP_000733.2:p.Leu442=
  • NP_001269384.1:p.Leu427=
  • NP_001334634.1:p.Leu283=
  • NP_001334635.1:p.Leu283=
  • NP_001334636.1:p.Leu244=
  • NP_001334637.1:p.Leu244=
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 ss76901821 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs56298562 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
ss76901821UUGC|CHRNA2_61311byFreqfwd/BC/Ttctgtgggcaccctctgcagccacggccactgcactctggggcctcaggtcccaaggctg10/01/0709/05/14129Genomicunknown
ss161151689PERLEGEN|IVD00719921byFreqrev/TA/Gcagccttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgcccacaga09/11/0909/05/14131Genomicunknown
ss3347726601000GENOMES|20100804_snps_6416201_chr8_27320636rev/A/Gcagccttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgcccacaga03/22/1103/22/11134Genomicunknown
ss342255718NHLBI-ESP|ESP2500-chr8-27320636byFreqrev/TA/Gcagccttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgcccacaga03/25/1109/05/14134Genomicunknown
ss4909626631000GENOMES|20110521_exome_470461_chr8_27320636rev/TA/Gcagccttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgcccacaga02/10/1202/21/12137Genomicunknown
ss491923164CLINSEQ_SNP|SNV-chr8-27376553byFreqrev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc03/06/1209/05/14137Genomicunknown
ss655076040SSMP|8_27320636rev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc12/14/1202/12/15138Genomicunknown
ss985336398EVA-GONL|EVA-GONL_rs56298562rev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc04/23/1404/25/14142Genomicunknown
ss1067496632JMKIDD_LAB|HGDP_exomes_chr8_27320636rev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc07/09/1407/09/14142Genomicunknown
ss13291528761000GENOMES|PHASE3_V1_41474901rev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc08/16/1408/16/14142Genomicunknown
ss1457613774CLINVAR|SCV000150679fwd/BC/Ttctgtgggcaccctctgcagccacggccactgcactctggggcctcaggtcccaaggctg11/23/1411/23/14142Genomicunknown
ss1584057807EVA_FINRISK|EVA_FINRISK_rs56298562rev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc02/27/1502/27/15144Genomicunknown
ss1594929040EVA_DECODE|EVA_DECODE_8_27376553_307751_rs56298562rev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc03/02/1503/03/15144Genomicunknown
ss1620263923EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_8_27320636_22938963rev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc03/04/1503/04/15144Genomicunknown
ss1663257956EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_8_27320636_22938963rev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc03/04/1503/04/15144Genomicunknown
ss1689143302EVA_EXAC|EVA_EXAC_4235183rev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc03/04/1503/04/15144Genomicunknown
ss1711197084EVA_MGP|EVA_XIMO_312844rev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc03/09/1503/09/15144Genomicunknown
ss1928625180WEILL_CORNELL_DGM|SNV:chr8:27320636rev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc10/16/1510/17/15147Genomicunknown
ss2025015245JJLAB|SNP5517800rev/TA/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc08/29/1608/30/16149Genomicunknown
ss2301783549HUMAN_LONGEVITY|HLI-8-27463119-G-Arev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc11/18/1611/18/16150Genomicunknown
ss2737071140GNOMAD|exomes_rs56298562rev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc05/17/1705/17/17151Genomicunknown
ss2748023006GNOMAD|coding_rs56298562rev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc05/17/1705/17/17151Genomicunknown
ss2864753981GNOMAD|rs56298562rev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc05/19/1705/19/17151Genomicunknown
ss3002899131SWEGEN|NC_000008.10:g.27320636G>Arev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc05/30/1705/30/17151Genomicunknown
ss3348109198CSHL|rs56298562rev/A/Gttgggacctgaggccccagagtgcagtggccgtggctgcagagggtgccc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs56298562|allelePos=502|totalLen=1003|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CCCTGCCTGC TCATCTCCTG CCTCACTGTG CTGGTCTTCT ACCTGCCCTC CGACTGCGGC
 GAGAAGATCA CGCTGTGCAT TTCGGTGCTG CTGTCACTCA CCGTCTTCCT GCTGCTCATC
 ACTGAGATCA TCCCGTCCAC CTCGCTGGTC ATCCCGCTCA TCGGCGAGTA CCTGCTGTTC
 ACCATGATCT TCGTCACCCT GTCCATCGTC ATCACCGTCT TCGTGCTCAA TGTGCACCAC
 CGCTCC
 CCCAGCACCC ACACCATGCC CCACTGGGTG CGGGGGGCCC TTCTGGGCTG TGTGCCCCGG
 TGGCTTCTGA TGAACCGGCC CCCACCACCC GTGGAGCTCT GCCACCCCCT ACGCCTGAAG
 CTCAGCCCCT CTTATCACTG GCTGGAGAGC AACGTGGATG CCGAGGAGAG GGAGGTGGTG
 GTGGAGGAGG AGGACAGATG GGCATGTGCA GGTCATGTGG CCCCCTCTGT GGGCACCCTC
 TGCAGCCACG GCCAC
 Y
 TGCACTCTGG GGCCTCAGGT CCCAAGGCTG AGGCTCTGCT GCAGGAGGGT GAGCTGCTGC
 TATCACCCCA CATGCAGAAG GCACTGGAAG GTGTGCACTA CATTGCCGAC CACCTGCGGT
 CTGAGGATGC TGACTCTTCG GTGCGTTGGG GTTGGGAGAG GCGCCAGCCT GGGTGGCCCC
 ACCAACTTAG CGGGGAACCA CCTTACCGCA GAGTGTGAGC TTGGGCAGCC CAGGCCCCTC
 TCGTGAAGGC CCACT
 TTCCTCAGTC ATGGTCCTTA GATGGAATAA ATAGCAAGAG AGCACATGTA GCTGGCCGCT
 TTGAGGACGT TTATTGGCAC GTGGCATGTT ACACACCACG GAGTCAGGCA TGAGCAGCTC
 AGCCTAACAG GGATCCTGAG AGCCGGAGAG GGAGGATCCC AGATGCTGAA CCCCGTGCCT
 CCCTCACGCC GCCAGCTCCC ACCATTGCCT TGGAGGTGGC GGCAGGCAGG GGGAGCATTT
 CAGGAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000008.9
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs56298562 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1329152876EAS 1008AF 1.00000000
EUR 1006AF 0.976100030.02390000
AFR 1322AF 0.999199990.00080000
AMR 694AF 0.988500000.01150000
SAS 978AF 0.965199950.03480000
ss161151689PGI_05_PANEL 860GF0.937209310.06279070 0.527089000.968604620.03139535
ss1689143302ExAc_Aggregated_Populations121412AF 0.977135720.02286430
ss342255718ESP_Cohort_Populations 4538GF0.969149410.03085059 0.479500000.984574680.01542530
ss491923164CSAgilent 1185GF0.932999970.06699999 1.000000000.966499980.03350000
ss76901821GAP 382IG0.958115160.036649220.005235600.004998000.976439770.02356021

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.045+/-0.1430000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES