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Reference SNP (refSNP) Cluster Report: rs4986988                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0168/84 (1000 Genomes)
T=0.0183/2299 (TOPMED)
HGVS Names
  • CM000670.2:g.18221704C>A
  • CM000670.2:g.18221704C>T
  • NC_000008.10:g.18079213C>T
  • NC_000008.11:g.18221704C>A
  • NC_000008.11:g.18221704C>T
  • NG_012245.2:g.56243C>A
  • NG_012245.2:g.56243C>T
  • NM_000662.7:c.-6-338C>A
  • NM_000662.7:c.-6-338C>T
  • NM_001160170.3:c.-6-338C>A
  • NM_001160170.3:c.-6-338C>T
  • NM_001160171.3:c.-6-338C>A
  • NM_001160171.3:c.-6-338C>T
  • NM_001160172.3:c.-6-338C>A
  • NM_001160172.3:c.-6-338C>T
  • NM_001160173.3:c.-6-338C>A
  • NM_001160173.3:c.-6-338C>T
  • NM_001160174.2:c.-344C>A
  • NM_001160174.2:c.-344C>T
  • NM_001160175.3:c.181-338C>A
  • NM_001160175.3:c.181-338C>T
  • NM_001160176.3:c.181-338C>A
  • NM_001160176.3:c.181-338C>T
  • NM_001160179.2:c.-6-338C>A
  • NM_001160179.2:c.-6-338C>T
  • NM_001291962.1:c.181-338C>A
  • NM_001291962.1:c.181-338C>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 ss5586786 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4986988 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
ss5586786SNP500CANCER|NAT1-03byFreqfwd/BC/Tttgcatgattctcctgcctacatcagaagagtttataagcctattttaaaggataccagt09/26/0204/07/04113Genomicunknown
ss12584636EGP_SNPS|NAT1-001726byFreqfwd/BC/Tttgcatgattctcctgcctacatcagaagagtttataagcctattttaaaggataccagt07/23/0304/07/04117Genomicunknown
ss32478875EGP_SNPS|NAT1-054488byFreqfwd/BC/Tttgcatgattctcctgcctacatcagaagagtttataagcctattttaaaggataccagt01/06/0511/02/06125Genomicunknown
ss75264441ILLUMINA|ILMN_Human_1M_rs4986988fwd/BC/Tttgcatgattctcctgcctacatcagaagagtttataagcctattttaaaggataccagt08/28/0708/29/07129Genomicunknown
ss84168360PHARMGKB_AB_DME|PS206058_PA147977699_301fwd/BC/Tttgcatgattctcctgcctacatcagaagagtttataagcctattttaaaggataccagt12/06/0712/09/07130Genomicunknown
ss119497108KRIBB_YJKIM|KHS1659355fwd/BC/Tttgcatgattctcctgcctacatcagaagagtttataagcctattttaaaggataccagt02/04/0902/04/09131Genomicunknown
ss160735777ILLUMINA|HumanOmni1-Quad_v1-0_B_rs4986988-128_T_R_1514219281rev/TA/Gactggtatcctttaaaataggcttataaactcttctgatgtaggcaggagaatcatgcaa08/04/0910/04/09131Genomicunknown
ss173903469ILLUMINA|Human1M-Duov3_B_rs4986988-128_T_R_1514219281rev/TA/Gactggtatcctttaaaataggcttataaactcttctgatgtaggcaggagaatcatgcaa10/01/0910/04/09132Genomicunknown
ss2343448871000GENOMES|pilot_1_CEU_3949516_chr8_18123493fwd/C/Tttgcatgattctcctgcctacatcagaagagtttataagcctattttaaaggataccagt05/01/1005/01/10132Genomicunknown
ss481125911ILLUMINA|HumanOmni2.5-4v1_B_rs4986988-128_T_R_1649462967fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata01/30/1210/29/16137Genomicunknown
ss482137006ILLUMINA|HumanOmni1-Quad_v1-0_C_rs4986988-131_T_R_1857739485fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata01/30/1208/28/15146Genomicunknown
ss536176364ILLUMINA|HumanOmni5-4v1_B_kgp7847600-0_T_R_1902837006fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata06/22/1208/29/15146Genomicunknown
ss655023154SSMP|8_18079213fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata12/14/1202/12/15138Genomicunknown
ss985254171EVA-GONL|EVA-GONL_rs4986988fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata04/23/1404/25/14142Genomicunknown
ss1075324494JMKIDD_LAB|HGDP_WGS_chr8_18079213fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata07/10/1407/11/14142Genomicunknown
ss13288470851000GENOMES|PHASE3_V1_41157924fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata08/16/1408/16/14142Genomicunknown
ss1431435945DDI|DDI_rs4986988fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata11/04/1411/05/14144Genomicunknown
ss1594843089EVA_DECODE|EVA_DECODE_8_18123493_221799_rs4986988fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata03/02/1503/03/15144Genomicunknown
ss1620096444EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_8_18079213_22757050fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata03/04/1503/04/15144Genomicunknown
ss1663090477EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_8_18079213_22757050fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata03/04/1503/04/15144Genomicunknown
ss1713019441EVA_SVP|EVA_SVP_713808fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata03/12/1503/12/15144Genomicunknown
ss1928543846WEILL_CORNELL_DGM|SNV:chr8:18079213fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata10/16/1510/17/15147Genomicunknown
ss1946231039ILLUMINA|HumanCoreExome-12v1-0_C_kgp7847600-0_T_R_1902837006fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata10/29/1510/29/15147Genomicunknown
ss1959092226ILLUMINA|kgp7847600-0_T_R_1902837006fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata11/13/1511/13/15147Genomicunknown
ss2024970093JJLAB|SNP5472648fwd/BC/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata08/29/1608/30/16149Genomicunknown
ss2301150625HUMAN_LONGEVITY|HLI-8-18221704-C-Tfwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata11/18/1611/18/16150Genomicunknown
ss2470808460TOPMED|8_18079213_C/Tfwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata11/20/1611/20/16150Genomicunknown
ss2634717586ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp7847600-0_T_R_190283700fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata02/02/1702/02/17151Genomicunknown
ss2708952059GRF|rs4986988fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata02/13/1702/13/17151Genomicunknown
ss2711131545ILLUMINA|Consortium-OncoArray_15047405_A_kgp7847600-0_T_R_1902837006fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata03/22/1703/22/17151Genomicunknown
ss2863914971GNOMAD|rs4986988fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata05/19/1705/19/17151Genomicunknown
ss2985432563AFFY|Axiom_PsorMich_Affx-31855722fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata05/24/1705/24/17151Genomicunknown
ss2986074617AFFY|Axiom_Smokesc1_Affx-31855722fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata05/24/1705/24/17151Genomicunknown
ss3002777594SWEGEN|NC_000008.10:g.18079213C>Tfwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata05/30/1705/30/17151Genomicunknown
ss3022824275ILLUMINA|MEGA_Consortium_v2_15070954_A2_kgp7847600-0_T_R_1902837006fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata06/28/1706/28/17151Genomicunknown
ss3555474968TOPMED|TOPMed_freeze_5?chr8:18,221,704-01fwd/A/Ctgattctcctgcctacatcagaagagtttataagcctattttaaaggata10/06/1710/06/17151Genomicunknown
ss3555474969TOPMED|TOPMed_freeze_5?chr8:18,221,704-02fwd/C/Ttgattctcctgcctacatcagaagagtttataagcctattttaaaggata10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4986988|allelePos=415|totalLen=1022|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=151
 AGCGAGTGTT TTTTTTTTGG TGTGTTTTTT TTTTTTTTAA ACCAACTAAT TTAAAATTGG
 AGCTCTCCCT CTGTACTTAC TGGGTCCTTT CTTTACTTTA GTTTTCCCAG GGCACTTACT
 ACAATCTAAC AGATTGCATG TTTTATCCAT GTATTCAATT TCCTATATAT GTCACTCCAA
 CTCCCACTAA AATATAAGAT TTTTGAGAGT AAGCAAGCAC TAGAACAGTA GGAAACACAT
 TATAGCTATT CAGTGAACTA TTTCTTGAGT TAATCAATCA ATGGATGAGT GAATCAATAC
 AGTTCTTTGA GCGGGAAACT TTGTATAAGG CTCAGCTAAA AGGGAAATTG AGTGGGTCAG
 GTACCACGGA TACTATACAC TCTATTGCAT GATTCTCCTG CCTACATCAG AAGA
 H
 GTTTATAAGC CTATTTTAAA GGATACCAGT TGGAATCTCT CTTTTATTAA TCACCAAGAG
 AACCATGAAC AAGCTGTTTA TCATTTGACT CATCATTTAA TCTTGATTTC CAGCTTCTCA
 CACTTGAAAG AAGACATAAT ACATTTCTCA CAGGATTCTG GGACTATTAA CTGAACTTAT
 GTGTGTAAAA GGAATTCATA CAATGAAAGC ACTAGAAATA ATTATTATAC TTATAACCAT
 TGTATTTTTA CATGTTTAAA ATATAGCCAT AATTAGCCTA CTCAAATCCA AGTGTAAAAG
 TAAWATGATT TGCTTTCGTT TTGTTTTCCT TGCTTAGGGG ATCATGGACA TTGAAGCATA
 TCTKGAAAGA ATTGGCTATA AGAAGTCTAG GAACAAATTG GACTTGGAAA CATTAACTGA
 CATTCTTCAA CACCAGATCY GAGCTGTTCC CTTTGAGAAC CTTAACATCC ATTGTGGGGA
 TGCCATGGAC TTAGGCTTAG AGGCCATTTT TGATCAAGTT GTGAGAAGAA ATYGGGGTGG
 ATGGTGTCTC CAGGTCAATC ATCTTCTGTA CTGGGCTCTG ACCACTATTG GTTTTGAGAC
 CACGATG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_030737.5
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.
SourceC/C
C/T
HWPC
T
ss12584636PDR90Global 176IG0.977272750.022727271.000000000.988636370.01136364
ss1328847085EAS 1008AF 0.994000020.00600000
EUR 1006AF 0.975100040.02490000
AFR 1322AF 0.997000040.00300000
AMR 694AF 0.987000050.01300000
SAS 978AF 0.959100010.04090000
ss234344887pilot_1_CEU_low_coverage_panel 120AF 0.975000020.02500000
ss32478875PDR90Global 172IG0.965116260.034883721.000000000.982558130.01744186
ss5586786P1 204AF0.980000020.020000001.000000000.990000010.01000000
CAUC1 62AF0.935000000.065000011.000000000.967999990.03200000
AFR1 48AF1.00000000 1.00000000
HISP1 46AF1.00000000 1.00000000
PAC1 48AF1.00000000 1.00000000
HapMap-CEUEuropean 226IG0.929203510.070796461.000000000.964601760.03539823
HapMap-HCBAsian 86IG1.00000000 1.00000000
HapMap-JPTAsian 172IG0.976744170.023255811.000000000.988372090.01162791
HapMap-YRISub-Saharan African 226IG0.991150440.008849561.000000000.995575250.00442478
HAPMAP-CHBAsian 82IG0.975609780.024390241.000000000.987804890.01219512
HAPMAP-CHD 170IG0.988235290.011764711.000000000.994117620.00588235
HAPMAP-GIH 176IG0.852272750.147727271.000000000.926136370.07386363
HAPMAP-LWK 180IG0.988888860.011111111.000000000.994444430.00555556
HAPMAP-MEX 100IG0.980000020.020000001.000000000.990000010.01000000
HAPMAP-MKK 286IG0.986014010.013986011.000000000.993007000.00699301
HAPMAP-TSI 174IG0.919540230.080459771.000000000.959770140.04022989
ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss84168360PA147977700 354AF 0.997175160.00282486

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.033+/-0.1240000

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

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