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Reference SNP (refSNP) Cluster Report: rs56240201                 
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:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0003/31 (ExAC)
A=0.0002/1 (1000 Genomes)
A=0.0011/14 (GO-ESP)
A=0.0005/67 (TOPMED)
HGVS Names
  • CM000677.2:g.74720599G>A
  • NC_000015.10:g.74720599G>A
  • NC_000015.9:g.75012940G>A
  • NC_000015.9:g.75012940G>C
  • NG_008431.2:g.3058G>A
  • NG_008431.2:g.3058G>C
  • NM_000499.4:c.1429C>G
  • NM_000499.4:c.1429C>T
  • NM_001319216.1:c.1342C>G
  • NM_001319216.1:c.1342C>T
  • NM_001319217.1:c.1429C>G
  • NM_001319217.1:c.1429C>T
  • NP_000490.1:p.Arg477Gly
  • NP_000490.1:p.Arg477Trp
  • NP_001306145.1:p.Arg448Gly
  • NP_001306145.1:p.Arg448Trp
  • NP_001306146.1:p.Arg477Gly
  • NP_001306146.1:p.Arg477Trp
  • XP_005254242.1:p.Arg477Gly
  • XP_005254242.1:p.Arg477Trp
  • XP_005254243.1:p.Arg477Gly
  • XP_005254243.1:p.Arg477Trp
  • XP_005254244.1:p.Arg449Gly
  • XP_005254244.1:p.Arg449Trp
  • XP_005254245.1:p.Arg448Gly
  • XP_005254245.1:p.Arg448Trp
  • XP_005254246.1:p.Arg216Gly
  • XP_005254246.1:p.Arg216Trp
  • XP_016877442.1:p.Arg449Trp
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 ss342408504 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs56240201 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
ss75252935ILLUMINA|ILMN_Human_1M_SNP14fwd/TA/Gtcacgcccagtggcacgctgaattccacccttgcagcaggatagccaggaagagaaagac08/28/0708/29/07129Genomicunknown
ss105434094AFFY_DM3_1|DMET3B10765fwd/TA/Gtcacgcccagtggcacgctgaattccacccttgcagcaggatagccaggaagagaaagac09/03/0809/03/08130Genomicunknown
ss161048992ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP14-0_B_R_1514230359rev/BC/Tgtctttctcttcctggctatcctgctgcaagggtggaattcagcgtgccactgggcgtga08/04/0910/05/09131Genomicunknown
ss169136103ILLUMINA|Human1M-Duov3_B_SNP14-unknown_B_R_1514230359rev/BC/Tgtctttctcttcctggctatcctgctgcaagggtggaattcagcgtgccactgggcgtga10/01/0910/01/09132Genomicunknown
ss201038159BUSHMAN|BUSHMAN-chr15-72799992fwd/C/Gtcacgcccagtggcacgctgaattccacccttgcagcaggatagccaggaagagaaagac02/16/1003/07/10132Genomicunknown
ss342408504NHLBI-ESP|ESP2500-chr15-75012940byFreqfwd/TA/Gtcacgcccagtggcacgctgaattccacccttgcagcaggatagccaggaagagaaagac03/25/1109/05/14134Genomicunknown
ss483025654ILLUMINA|HumanOmni1-Quad_v1-0_C_SNP14-0_B_R_1852986282fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga01/30/1208/28/15146Genomicunknown
ss4890555521000GENOMES|20110521_exome_201462_chr15_75012940fwd/TA/Gtcacgcccagtggcacgctgaattccacccttgcagcaggatagccaggaagagaaagac02/10/1202/13/12137Genomicunknown
ss491497244EXOME_CHIP|nonsyn_213470_chr_15_75012940fwd/TA/Gtcacgcccagtggcacgctgaattccacccttgcagcaggatagccaggaagagaaagac03/05/1203/05/12137Genomicunknown
ss537652764ILLUMINA|HumanOmni5-4v1_B_SNP14-0_B_R_1852986282fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga06/22/1208/29/15146Genomicunknown
ss780710880ILLUMINA|HumanOmni25Exome-8v1_A_exm1176857-0_B_R_1922857664fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga05/30/1307/10/15146Genomicunknown
ss783385697ILLUMINA|HumanOmniExpressExome-8v1_A_exm1176857-0_B_R_1922857664fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga05/31/1306/18/15146Genomicunknown
ss13541266301000GENOMES|PHASE3_V1_67486059fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga08/16/1408/16/14142Genomicunknown
ss1691925228EVA_EXAC|EVA_EXAC_7235673fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga03/04/1503/04/15144Genomicunknown
ss1752171226ILLUMINA|OmniExpressExome-8v1-1_B_exm1176857-0_B_R_1922857664fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga05/27/1506/09/15146Genomicunknown
ss1917898831ILLUMINA|HumanExome-12v1-1_B_exm1176857-0_B_R_1922857664fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga10/16/1510/16/15147Genomicunknown
ss1935358391WEILL_CORNELL_DGM|SNV:chr15:75012940fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga10/16/1510/18/15147Genomicunknown
ss1946398541ILLUMINA|HumanCoreExome-12v1-0_C_exm1176857-0_B_R_1922857664fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga10/29/1510/29/15147Genomicunknown
ss1959626324ILLUMINA|exm1176857-0_B_R_1922857664fwd/TA/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga11/13/1511/13/15147Genomicunknown
ss2208163229HUMAN_LONGEVITY|HLI-15-74720599-G-Afwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga11/18/1611/18/16150Genomicunknown
ss2372615593TOPMED|15_75012940_G/Afwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga11/19/1611/19/16150Genomicunknown
ss2633251257ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SNP14-0_B_R_1852986282fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga02/02/1702/02/17151Genomicunknown
ss2710820347ILLUMINA|Consortium-OncoArray_15047405_A_rs56240201-131_B_R_2060347452fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga03/22/1703/22/17151Genomicunknown
ss2741397931GNOMAD|exomes_rs56240201fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga05/17/1705/17/17151Genomicunknown
ss2749350456GNOMAD|coding_rs56240201fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga05/17/1705/17/17151Genomicunknown
ss2936799542GNOMAD|rs56240201fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga05/23/1705/23/17151Genomicunknown
ss3021649351ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm1176857-0_B_R_1922857664fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga06/28/1706/28/17151Genomicunknown
ss3029638383CSIRBIOHTS|NM_000499.3:g.75012940G>Afwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga07/28/1707/28/17151Genomicunknown
ss3231998281TOPMED|TOPMed_freeze_5?chr15:74,720,599fwd/A/Gcccagtggcacgctgaattccacccttgcagcaggatagccaggaagaga10/01/1710/01/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs56240201|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 ACAGCCCAGA TAGCAAAACT GCAGCCAGAT CAGTGTCTAT GAGTTTCAGG CTGAACCTTA
 GACCACATAG GCCAGCCTGC TGGTCTGGCT GCCCAACCAG ACCAGGTAGA CAGAGTCTAG
 GCCTCAGGGC TCTCAAGCAC CTAAGAGCGC AGCTGCATTT GGAAGTGCTC ACAGCAGGCA
 TGCTTCATGG TTAGCCCATA GATGGGGGTC ATGTCCACCT TCACGCCCAG TGGCACGCTG
 AATTCCACCC
 R
 TTGCAGCAGG ATAGCCAGGA AGAGAAAGAC CTCCCAGCGG GCAATGGTCT CACCGATACA
 CTTCCGCTTG CCCATGCCAA AGATAATCAC CTTCTCACTT AACACCTTGT CGATAGCACC
 ATCAGGGGTG AGAAACCGTT CAGGTAGGAA CTCAGATGGG TTGACCCATA GCTTCCTGTA
 ACCAGAGGGA GACAGCTGAA GTGGCAGTTC AGGGCTCAGA AGTGTCAAGT GAGTGGAGCT
 CCAGCCCCAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000015
dbSNP Blast Analysis
3D structure mapping
NP_000490  

  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/G
G/G
HWPA
G
ss1354126630EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.000800000.99919999
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1691925228ExAc_Aggregated_Populations121410AF 0.000255330.99974465
ss342408504ESP_Cohort_Populations 4552GF 0.003075570.996924401.000000000.001537790.99846220

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.001+/-0.0160000

  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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