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Reference SNP (refSNP) Cluster Report: rs5916687                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:114/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Association:NHGRI GWAS PheGenI
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=0.1176/444 (1000 Genomes)
A=0.1976/24806 (TOPMED)
HGVS Names
  • CM000685.2:g.4678097G>A
  • NC_000023.10:g.4596138G>A
Links , Linkout
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 ss21005777 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5916687 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
ss8191074SC_SNP|NT_011649.11_921386fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt04/16/0310/10/03114Genomicunknown
ss21005777SSAHASNP|WGSA-200403-chrX.chrX.NT_011757.13_662782byFreqfwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt03/19/0410/26/06121Genomicunknown
ss66751163ILLUMINA|HumanHap300v1.1_rs5916687fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt11/09/0611/09/06127Genomicunknown
ss67424909ILLUMINA|HumanHap550v1.1_rs5916687fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt11/14/0611/14/06127Genomicunknown
ss67783994ILLUMINA|HumanHap650Yv1.0_rs5916687fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt11/14/0611/14/06127Genomicunknown
ss70849345ILLUMINA|HumanHap550v3.0__rs5916687rev/BC/Taaaagtgctctaattttatctgttcttttcaatagctatcacaaattttcatttactcat04/20/0703/31/08130Genomicunknown
ss71434425ILLUMINA|HumanHap650Yv3.0_rs5916687fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt04/23/0704/23/07127Genomicunknown
ss75727432ILLUMINA|ILMN_Human_1M_rs5916687fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt08/28/0708/29/07129Genomicunknown
ss79211117ILLUMINA|HumanHap300v2.0_rs5916687fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt04/18/0711/18/07130Genomicunknown
ss84428911KRIBB_YJKIM|KHS708758fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt12/04/0712/07/07130Genomicunknown
ss94219237BCMHGSC_JDW|JWB-2664730fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt02/26/0803/06/08129Genomicunknown
ss122482395ILLUMINA|HumanCNV370v1_C_rs5916687fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt04/14/0904/15/09131Genomicunknown
ss144182912ENSEMBL|ENSSNP5569862fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt12/08/0810/17/09131Genomicunknown
ss144471313ENSEMBL|ENSSNP13812127fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt06/05/0906/06/09131Genomicunknown
ss154343448ILLUMINA|Human610_Quadv1_B_rs5916687-127_B_R_1501807346rev/BC/Taaaagtgctctaattttatctgttcttttcaatagctatcacaaattttcatttactcat06/18/0906/20/09131Genomicunknown
ss159520015ILLUMINA|Human660W-Quad_v1_A_rs5916687-128_B_R_1501807346rev/BC/Taaaagtgctctaattttatctgttcttttcaatagctatcacaaattttcatttactcat07/06/0907/07/09131Genomicunknown
ss160749546ILLUMINA|HumanOmni1-Quad_v1-0_B_rs5916687-128_B_R_1512175593rev/BC/Taaaagtgctctaattttatctgttcttttcaatagctatcacaaattttcatttactcat08/04/0910/04/09131Genomicunknown
ss163012852COMPLETE_GENOMICS|NA07022_36_chrX_4606138fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt09/29/0909/29/09132Genomicunknown
ss166052497COMPLETE_GENOMICS|NA20431_36_chrX_4606138fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt09/30/0909/30/09132Genomicunknown
ss172053938ILLUMINA|HumanCNV370-Quadv3_C_rs5916687-127_B_R_1501807346rev/BC/Taaaagtgctctaattttatctgttcttttcaatagctatcacaaattttcatttactcat10/01/0910/04/09132Genomicunknown
ss173938016ILLUMINA|Human1M-Duov3_B_rs5916687-127_B_R_1501807346rev/BC/Taaaagtgctctaattttatctgttcttttcaatagctatcacaaattttcatttactcat10/01/0910/04/09132Genomicunknown
ss294446743PJP|SNP_3953101_chrX_4606138fwd/A/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt01/21/1101/21/11134Genomicunknown
ss3412777561000GENOMES|20100804_snps_29460_chrX_4596138fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt03/23/1103/23/11134Genomicunknown
ss481168196ILLUMINA|HumanOmni2.5-4v1_B_rs5916687-128_B_R_1649339991fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca01/30/1210/29/16137Genomicunknown
ss481190712ILLUMINA|HumanOmniExpress-12v1_C_rs5916687-131_B_R_1856922919fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca01/30/1210/27/16137Genomicunknown
ss482178499ILLUMINA|HumanOmni1-Quad_v1-0_C_rs5916687-131_B_R_1865278045fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca01/30/1208/28/15146Genomicunknown
ss482749468ILLUMINA|HumanOmni2.5-4v1_D_kgp22782406-0_B_R_1860537647fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca01/30/1210/28/16137Genomicunknown
ss484379185ILLUMINA|HumanOmni2.5-4v1_B_SNP23-4606138-0_B_R_1650701803fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca01/30/1210/29/16137Genomicunknown
ss485379307ILLUMINA|HumanOmni2.5-4v1_D_rs5916687-131_B_R_1856922919fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca01/30/1210/28/16137Genomicunknown
ss491574773EXOME_CHIP|.GWAS._290999_chr_X_4596138fwd/TA/Gatgagtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagcactttt03/05/1203/06/12137Genomicunknown
ss534763558ILLUMINA|HumanOmni5-4v1_B_kgp22782406-0_B_R_1860537647fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca06/22/1208/28/15146Genomicunknown
ss662678867SSMP|X_4596138fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca12/14/1202/14/15138Genomicunknown
ss778931946ILLUMINA|HumanOmni25Exome-8v1_A_rs5916687-131_B_R_1865278045fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/30/1307/09/15146Genomicunknown
ss780063799ILLUMINA|HumanOmni25Exome-8v1_A_kgp22782406-0_B_R_1860537647fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/30/1307/09/15146Genomicunknown
ss780685670ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs5916687-131_B_R_1990483957fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/30/1307/09/15146Genomicunknown
ss781864863ILLUMINA|HumanOmni2.5-4v1_H_kgp22782406-0_B_R_1860537647fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/30/1307/28/15146Genomicunknown
ss783135214ILLUMINA|HumanOmni2.5-4v1_H_rs5916687-131_B_R_1856922919fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/30/1307/28/15146Genomicunknown
ss783359166ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs5916687-131_B_R_1990483957fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/31/1306/19/15146Genomicunknown
ss784091584ILLUMINA|HumanOmniExpressExome-8v1_A_rs5916687-131_B_R_1885471025fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/31/1306/19/15146Genomicunknown
ss825541635ILLUMINA|HumanCNV370v1_C_rs5916687-121_B_R_IFB1136155345:0fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca06/24/1311/21/14147Genomicunknown
ss832394180ILLUMINA|HumanOmniExpress-12v1_H_rs5916687-131_B_R_1856922919fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca09/17/1306/19/15146Genomicunknown
ss834393508ILLUMINA|HumanOmni2.5-8v1_A_rs5916687-131_B_R_1865278045fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca09/18/1307/28/15146Genomicunknown
ss835545312ILLUMINA|HumanOmni2.5-8v1_A_kgp22782406-0_B_R_1860537647fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca09/18/1307/28/15146Genomicunknown
ss1082770138JMKIDD_LAB|HGDP_WGS_chrX_4596138fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca07/10/1407/12/14142Genomicunknown
ss15533770631000GENOMES|PHASE3_chrX_150887byFreqfwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca08/16/1408/07/15144Genomicunknown
ss1583315509EVA_GENOME_DK|EVA_GENOME_DK_snv_rs5916687fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca02/19/1502/20/15144Genomicunknown
ss1640264518EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_X_4596138_44946604fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca03/04/1503/04/15144Genomicunknown
ss1683258551EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_X_4596138_44946604fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca03/04/1503/04/15144Genomicunknown
ss1752807479ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs5916687-131_B_R_1990483957fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/27/1506/09/15146Genomicunknown
ss1752807480ILLUMINA|OmniExpressExome-8v1-1_B_rs5916687-131_B_R_1885471025fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/27/1506/09/15146Genomicunknown
ss1917715793ILLUMINA|HumanExome-12v1-1_B_exm-rs5916687-131_B_R_1990483957fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca10/16/1510/16/15147Genomicunknown
ss1939111555WEILL_CORNELL_DGM|SNV:chrX:4596138fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca10/16/1510/19/15147Genomicunknown
ss1945967210ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs5916687-131_B_R_1990483957fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca10/29/1510/29/15147Genomicunknown
ss1958167470ILLUMINA|exm-rs5916687-131_B_R_1990483957fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca11/13/1511/13/15147Genomicunknown
ss1971337258GENOMED|rs5916687fwd/TA/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca02/16/1602/16/16147Genomicunknown
ss2158931496USC_VALOUEV|NC_000023.10:g.4596138G>Afwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca11/17/1611/17/16150Genomicunknown
ss2315432081HUMAN_LONGEVITY|HLI-X-4678097-G-Afwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca11/18/1611/18/16150Genomicunknown
ss2634935133ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SoL-rs5916687-131_B_R_2131fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca02/02/1702/02/17151Genomicunknown
ss2634935134ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp22782406-0_B_R_18605376fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca02/02/1702/02/17151Genomicunknown
ss2634935135ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs5916687-131_B_R_18854710fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca02/02/1702/02/17151Genomicunknown
ss2634935136ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs5916687-131_B_R_2130fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca02/02/1702/02/17151Genomicunknown
ss2976158175GNOMAD|rs5916687fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/23/1705/23/17151Genomicunknown
ss2985480027AFFY|Axiom_PsorMich_Affx-34905817fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/24/1705/24/17151Genomicunknown
ss3019580886SWEGEN|NC_000023.10:g.4596138G>Afwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca05/30/1705/30/17151Genomicunknown
ss3022986870ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs5916687-138_B_R_2264362226fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca06/28/1706/28/17151Genomicunknown
ss3028998628BIOINF_KMB_FNS_UNIBA|X.4678097G>Afwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca07/05/1707/05/17151Genomicunknown
ss3604524453TOPMED|TOPMed_freeze_5?chrX:4,678,097fwd/A/Gtaaatgaaaatttgtgatagctattgaaaagaacagataaaattagagca10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs5916687|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 ATACGTAAAT AACAGAAGCA CACTAGCTTg gtgcgtggct tgtgctggta atcccagctc
 tttagcagac ccagtttgga ggattgcttg agcccaagcg tttgagagca gcctgggaaa
 catagcaaat tcccatcttt ataaaaaata aacaaaatta gctgggtgtg gtgacacacg
 cctgtagtcc cagctactcg gggaggctga ggtgggagga ttgcttgagc ccaggatgtt
 gagcctaccg tgagctagga ttgcaccact gcactccagc ctgggcaaca gagcaagagc
 tagtctcaaa cgaaacaaaa caaaaaGCAC TCTTCTAAAA TGAATACCGA TTGCAGCCTA
 AAAAGCAAAA TACTAAAGTA ATTTCAAGAA AAATTAGAGA GCACATGAGA ATGCCTTTTA
 TTTCTATTAT TATCCAACGA CTTCGGGAAG ATTGTGGCAA ATGCAGTGAA ATGAGTAAAT
 GAAAATTTGT GATAGCTATT
 R
 GAAAAGAACA GATAAAATTA GAGCACTTTT GCTGATAGCA TGAATGTTTA CCTGAGAAAA
 TCTAAAAACC TATTCGAAAA ATAAGGTAAT TTGGTAAAAT TGCTGAATAC AAAGTAAATA
 AACAAAAATT ATTAGTGTTT TTTACATACT GCAGTAGGAA CCTAGAAAGC AATATGGGAG
 CATTCTATTG AAAATCCAAT AATTATGTTA AAAAACTTAG GAGTGCATAT AATAAGAGGG
 GCGCTGGGAA GAAATACATT GAATTAAACT GAAACACGGA ATACCCAAAC AAATGGAAGT
 ACATGTTATA TCCTCAAATG CTTAAATTAT ACATCACAAA AATGCCAACT CCACCAAAAT
 TGATGGATGA ATCAATTGTC ATCCAATTGC CAATCATAAC AAGGTGTTTA ATCTTTTGCA
 TTGTAGAAAA TGATCTCACA GTTCATATAG AAAGATGTAT TATACAAGTA TAGTTAGGAA
 ATCAATGAGA GAAATAATAC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011757
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
A/A
A/G
G/G
HWPA
G
ss144182912ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss144471313ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss1553377063EAS 1008AF 1.00000000
EUR 1006AF 0.213700000.78630000
AFR 1322AF 0.045400000.95459998
AMR 694AF 0.118200000.88180000
SAS 978AF 0.089000000.91100001
ss163012852CEUEuropean 1IG1.00000000 1.00000000
ss166052497PGP 1IG1.00000000 1.00000000
ss21005777HapMap-CEUEuropean 224IG 0.223214280.142857150.633928600.001000000.294642870.70535713
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 172IG 0.011627910.988372091.000000000.005813950.99418604
HapMap-YRISub-Saharan African 226IG 0.026548670.973451321.000000000.013274340.98672569
HAPMAP-ASW 98IG 0.040816330.081632650.877551020.002501000.081632650.91836733
HAPMAP-GIH 176IG 0.113636370.147727270.738636370.001000000.187500000.81250000
HAPMAP-LWK 180IG 0.011111110.011111110.977777780.001000000.016666670.98333335
HAPMAP-MEX 100IG 0.040000000.120000000.839999970.020022000.100000000.89999998
HAPMAP-MKK 282IG 0.042553190.056737590.900709210.001000000.070921990.92907804
HAPMAP-TSI 174IG 0.252873570.229885060.517241360.001000000.367816090.63218391

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.208+/-0.2460000ALFRED: The Allele Frequency Database

  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

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