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Reference SNP (refSNP) Cluster Report: rs4986990                 
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/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.0209/2540 (ExAC)
A=0.0170/85 (1000 Genomes)
A=0.0171/222 (GO-ESP)
A=0.0183/2299 (TOPMED)
HGVS Names
  • CM000670.2:g.18222506G>A
  • NC_000008.10:g.18080015G>A
  • NC_000008.11:g.18222506G>A
  • NG_012245.2:g.57045G>A
  • NM_000662.7:c.459G>A
  • NM_001160170.3:c.459G>A
  • NM_001160171.3:c.459G>A
  • NM_001160172.3:c.459G>A
  • NM_001160173.3:c.459G>A
  • NM_001160174.2:c.459G>A
  • NM_001160175.3:c.645G>A
  • NM_001160176.3:c.645G>A
  • NM_001160179.2:c.459G>A
  • NM_001291962.1:c.645G>A
  • NP_000653.3:p.Thr153=
  • NP_001153642.1:p.Thr153=
  • NP_001153643.1:p.Thr153=
  • NP_001153644.1:p.Thr153=
  • NP_001153645.1:p.Thr153=
  • NP_001153646.1:p.Thr153=
  • NP_001153647.1:p.Thr215=
  • NP_001153648.1:p.Thr215=
  • NP_001153651.1:p.Thr153=
  • NP_001278891.1:p.Thr215=
  • XP_005273734.1:p.Thr215=
  • XP_005273735.1:p.Thr153=
  • XP_005273736.1:p.Thr153=
  • XP_006716473.1:p.Thr153=
  • XP_011542989.1:p.Thr215=
  • XP_011542990.1:p.Thr215=
  • XP_011542991.1:p.Thr153=
  • XP_016869436.1:p.Thr215=
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 ss32478881 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4986990 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
ss5586788SNP500CANCER|NAT1-06byFreqfwd/TA/Ggcctcaggtgccttgtrtcttccgtttgacgaagagaatggattctggtatctagaccaa09/26/0204/07/04113Genomicunknown
ss24180119PERLEGEN|afd4578698fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa08/10/0408/21/04123Genomicunknown
ss32478881EGP_SNPS|NAT1-055290byFreqfwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa01/06/0511/02/06125Genomicunknown
ss75232327ILLUMINA|ILMN_Human_1M_rs4986990fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa08/28/0708/29/07129Genomicunknown
ss84168371PHARMGKB_AB_DME|PS206058_PA147979304_301fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa12/06/0712/09/07130Genomicunknown
ss119497110KRIBB_YJKIM|KHS1659357fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa02/04/0902/04/09131Genomicunknown
ss154334569ILLUMINA|Human610_Quadv1_B_rs4986990-128_T_F_1514219283fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa06/18/0906/20/09131Genomicunknown
ss159511092ILLUMINA|Human660W-Quad_v1_A_rs4986990-128_T_F_1514219283fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa07/06/0907/07/09131Genomicunknown
ss160735779ILLUMINA|HumanOmni1-Quad_v1-0_B_rs4986990-128_T_F_1514219283fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa08/04/0910/04/09131Genomicunknown
ss173903473ILLUMINA|Human1M-Duov3_B_rs4986990-128_T_F_1514219283fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa10/01/0910/04/09132Genomicunknown
ss2343448901000GENOMES|pilot_1_CEU_3949519_chr8_18124295fwd/A/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa05/01/1005/01/10132Genomicunknown
ss244302411ILLUMINA|CVDSNP55v1_A_rs4986990fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa06/10/1006/10/10132Genomicunknown
ss342253583NHLBI-ESP|ESP2500-chr8-18080015byFreqfwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa03/25/1109/05/14134Genomicunknown
ss481125921ILLUMINA|HumanOmni2.5-4v1_B_rs4986990-128_T_F_1649462973fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag01/30/1210/29/16137Genomicunknown
ss481148073ILLUMINA|HumanOmniExpress-12v1_C_rs4986990-131_T_F_1857739487fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag01/30/1210/27/16137Genomicunknown
ss482137011ILLUMINA|HumanOmni1-Quad_v1-0_C_rs4986990-131_T_F_1865185099fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag01/30/1208/28/15146Genomicunknown
ss485358036ILLUMINA|HumanOmni2.5-4v1_D_rs4986990-131_T_F_1857739487fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag01/30/1210/28/16137Genomicunknown
ss4909607071000GENOMES|20110521_exome_468505_chr8_18080015fwd/TA/Ggcctcaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctagaccaa02/10/1202/21/12137Genomicunknown
ss491921828CLINSEQ_SNP|SNV-chr8-18124295byFreqfwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag03/06/1209/05/14137Genomicunknown
ss537302784ILLUMINA|HumanOmni5-4v1_B_rs4986990-131_T_F_1889936636fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag06/22/1208/29/15146Genomicunknown
ss655023160SSMP|8_18080015fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag12/14/1202/12/15138Genomicunknown
ss778927511ILLUMINA|HumanOmni25Exome-8v1_A_rs4986990-131_T_F_1869436587fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/30/1307/10/15146Genomicunknown
ss783124727ILLUMINA|HumanOmni2.5-4v1_H_rs4986990-131_T_F_1857739487fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/30/1307/29/15146Genomicunknown
ss784081380ILLUMINA|HumanOmniExpressExome-8v1_A_rs4986990-131_T_F_1889936636fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/31/1306/19/15146Genomicunknown
ss832383550ILLUMINA|HumanOmniExpress-12v1_H_rs4986990-131_T_F_1857739487fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag09/17/1306/19/15146Genomicunknown
ss834389012ILLUMINA|HumanOmni2.5-8v1_A_rs4986990-131_T_F_1869436587fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag09/18/1307/29/15146Genomicunknown
ss985254177EVA-GONL|EVA-GONL_rs4986990fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag04/23/1404/25/14142Genomicunknown
ss1067495856JMKIDD_LAB|HGDP_exomes_chr8_18080015fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag07/09/1407/09/14142Genomicunknown
ss1075324499JMKIDD_LAB|HGDP_WGS_chr8_18080015fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag07/10/1407/11/14142Genomicunknown
ss13288471141000GENOMES|PHASE3_V1_41157953fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag08/16/1408/16/14142Genomicunknown
ss1431435948DDI|DDI_rs4986990fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag11/04/1411/05/14144Genomicunknown
ss1584057281EVA_FINRISK|EVA_FINRISK_rs4986990fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag02/27/1502/27/15144Genomicunknown
ss1594843095EVA_DECODE|EVA_DECODE_8_18124295_221805_rs4986990fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag03/02/1503/03/15144Genomicunknown
ss1620096456EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_8_18080015_22757062fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag03/04/1503/04/15144Genomicunknown
ss1663090489EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_8_18080015_22757062fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag03/04/1503/04/15144Genomicunknown
ss1689107665EVA_EXAC|EVA_EXAC_4197072fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag03/04/1503/04/15144Genomicunknown
ss1711194376EVA_MGP|EVA_XIMO_310136fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag03/09/1503/09/15144Genomicunknown
ss1713019445EVA_SVP|EVA_SVP_713812fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag03/12/1503/12/15144Genomicunknown
ss1752722035ILLUMINA|OmniExpressExome-8v1-1_B_rs4986990-131_T_F_2087479467fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/27/1506/09/15146Genomicunknown
ss1928543853WEILL_CORNELL_DGM|SNV:chr8:18080015fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag10/16/1510/17/15147Genomicunknown
ss1946231049ILLUMINA|HumanCoreExome-12v1-0_C_rs4986990-131_T_F_2087479467fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag10/29/1510/29/15147Genomicunknown
ss1959092245ILLUMINA|rs4986990-131_T_F_1889936636fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag11/13/1511/13/15147Genomicunknown
ss2024970097JJLAB|SNP5472652fwd/TA/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag08/29/1608/30/16149Genomicunknown
ss2301150662HUMAN_LONGEVITY|HLI-8-18222506-G-Afwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag11/18/1611/18/16150Genomicunknown
ss2470808517TOPMED|8_18080015_G/Afwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag11/20/1611/20/16150Genomicunknown
ss2634717602ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_SoL-rs4986990-131_B_R_2131fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag02/02/1702/02/17151Genomicunknown
ss2634717603ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs4986990-131_T_F_20874794fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag02/02/1702/02/17151Genomicunknown
ss2635180424ILLUMINA|Cancer_BeadChip_11459870_A_rs4986990-128_T_F_1649462973fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag02/02/1702/02/17151Genomicunknown
ss2708952063GRF|rs4986990fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag02/13/1702/13/17151Genomicunknown
ss2711131556ILLUMINA|Consortium-OncoArray_15047405_A_rs4986990-131_T_F_2087479467fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag03/22/1703/22/17151Genomicunknown
ss2737016411GNOMAD|exomes_rs4986990fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/17/1705/17/17151Genomicunknown
ss2748005860GNOMAD|coding_rs4986990fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/17/1705/17/17151Genomicunknown
ss2863915035GNOMAD|rs4986990fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/19/1705/19/17151Genomicunknown
ss2985432568AFFY|Axiom_PsorMich_Affx-31855741fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/24/1705/24/17151Genomicunknown
ss2986074622AFFY|Axiom_Smokesc1_Affx-31855741fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/24/1705/24/17151Genomicunknown
ss3002777604SWEGEN|NC_000008.10:g.18080015G>Afwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag05/30/1705/30/17151Genomicunknown
ss3022824288ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs4986990-138_T_F_2264369206fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag06/28/1706/28/17151Genomicunknown
ss3555475120TOPMED|TOPMed_freeze_5?chr8:18,222,506fwd/A/Gaggtgccttgtgtcttccgtttgacgaagagaatggattctggtatctag10/06/1710/06/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4986990|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 TCTCCAGGTC AATCATCTTC TGTACTGGGC TCTGACCACT ATTGGTTTTG AGACCACGAT
 GTTGGGAGGG TATGTTTACA GCACTCCAGC CAAAAAATAC AGCACTGGCA TGATTCACCT
 TCTCCTGCAG GTGACCATTG ATGGCAGGAA CTACATTGTC GATGCTGGGT TTGGACGCTC
 ATACCAGATG TGGCAGCCTC TGGAGTTAAT TTCTGGGAAG GATCAGCCTC AGGTGCCTTG
 TGTCTTCCGT TTGAC
 R
 GAAGAGAATG GATTCTGGTA TCTAGACCAA ATCAGAAGGG AACAGTACAT TCCAAATGAA
 GAATTTCTTC ATTCTGATCT CCTAGAAGAC AGCAAATACC GAAAAATCTA CTCCTTTACT
 CTTAAGCCTC GAACAATTGA AGATTTTGAG TCTATGAATA CATACCTGCA GACATCTCCA
 TCATCTGTGT TTACTAGTAA ATCATTTTGT TCCTTGCAGA CCCCAGATGG GGTTCACTGT
 TTGGTGGGCT TCACC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_030737.5
dbSNP Blast Analysis
UniGene Cluster ID
155956
3D structure mapping
NP_000653  NP_001153642  NP_001153643  NP_001153644  NP_001153645  NP_001153646  NP_001153647  NP_001153648  NP_001153651  

  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
ss1328847114EAS 1008AF 0.006900000.99309999
EUR 1006AF 0.024900000.97510004
AFR 1322AF 0.003000000.99700004
AMR 694AF 0.013000000.98700005
SAS 978AF 0.040900000.95910001
ss1689107665ExAc_Aggregated_Populations121412AF 0.020928740.97907126
ss234344890pilot_1_CEU_low_coverage_panel 120AF 0.016666670.98333335
ss24180119AFD_EUR_PANELEuropean 48IG 1.00000000 1.00000000
AFD_AFR_PANELAfrican American 46IG 1.00000000 1.00000000
AFD_CHN_PANELAsian 48IG 0.041666670.958333311.000000000.020833330.97916669
ss32478881PDR90Global 176IG 0.034090910.965909061.000000000.017045460.98295456
HapMap-CEUEuropean 226IG 0.070796460.929203511.000000000.035398230.96460176
HapMap-HCBAsian 86IG 1.00000000 1.00000000
HapMap-JPTAsian 172IG 0.023255810.976744171.000000000.011627910.98837209
HapMap-YRISub-Saharan African 226IG 0.008849560.991150441.000000000.004424780.99557525
HAPMAP-CHBAsian 82IG 0.048780490.951219501.000000000.024390240.97560978
HAPMAP-CHD 170IG 0.011764710.988235291.000000000.005882350.99411762
HAPMAP-GIH 176IG 0.147727270.852272751.000000000.073863630.92613637
HAPMAP-LWK 178IG 0.011235960.988764051.000000000.005617980.99438202
HAPMAP-MEX 100IG 0.020000000.980000021.000000000.010000000.99000001
HAPMAP-MKK 280IG 0.014285710.985714261.000000000.007142860.99285716
HAPMAP-TSI 176IG 0.079545450.920454561.000000000.039772730.96022725
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss342253583ESP_Cohort_Populations 4550GF0.000879120.028131870.970988990.050043000.014945060.98505497
ss491921828CSAgilent 1315GF0.002000000.050000000.948000010.250592000.027000000.97299999
ss5586788P1 204AF 0.020000000.980000021.000000000.010000000.99000001
CAUC1 62AF 0.065000010.935000001.000000000.032000000.96799999
AFR1 48AF 1.00000000 1.00000000
HISP1 46AF 1.00000000 1.00000000
PAC1 48AF 1.00000000 1.00000000
ss84168371PA147979305 360AF 0.002777780.99722224

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.041+/-0.1370000

  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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