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Reference SNP (refSNP) Cluster Report: rs7187889                 ** With Likely benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
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:With Likely benign allele [ClinVar]
MAF/MinorAlleleCount:A=0.0139/1619 (ExAC)
A=0.0439/220 (1000 Genomes)
A=0.0497/646 (GO-ESP)
A=0.0462/5803 (TOPMED)
HGVS Names
  • CM000678.2:g.88836235G>A
  • NC_000016.10:g.88836235G>A
  • NC_000016.9:g.88902643G>A
  • NG_008667.1:g.25732C>T
  • NM_000512.4:c.599C>T
  • NM_001323543.1:c.44C>T
  • NM_001323544.1:c.617C>T
  • NP_000503.1:p.Thr200Met
  • NP_001310472.1:p.Thr15Met
  • NP_001310473.1:p.Thr206Met
  • XP_005256358.1:p.Thr200Met
  • XP_005256359.1:p.Thr206Met
  • XP_005256360.1:p.Thr15Met
  • XP_011521284.1:p.Thr206Met
  • XP_016878600.1:p.Thr206Met
  • XP_016878601.1:p.Thr206Met
  • XP_016878602.1:p.Thr15Met
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 ss10811144 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7187889 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
ss10811144BCM_SSAHASNP|chr16.NT_010542.13_460464byFreqfwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat06/30/0310/25/06116Genomicunknown
ss48417370APPLERA_GI|hCV25995475byFreqrev/BC/Tattatgaagaatttcctattaatctgaagagggggaagccaacctcacccagatctacct09/28/0511/03/06126Genomicunknown
ss69355253PERLEGEN|PGP04755369byFreqfwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat01/30/0703/31/08127Genomicunknown
ss74870148ILLUMINA|ILMN_Human_1M_rs7187889fwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat08/28/0708/29/07129Genomicunknown
ss119545562KRIBB_YJKIM|KHS1707809fwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat02/04/0902/05/09131Genomicunknown
ss159733817SEATTLESEQ|GALNS-87430144fwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat07/10/0907/10/09131Genomicunknown
ss161057728ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP16-87430144-0_B_R_1588118453rev/BC/Tattatgaagaatttcctattaatctgaagagggggaagccaacctcacccagatctacct08/04/0910/05/09131Genomicunknown
ss174280836ILLUMINA|Human1M-Duov3_B_rs7187889-127_B_R_1513909967rev/BC/Tattatgaagaatttcctattaatctgaagagggggaagccaacctcacccagatctacct10/01/0910/04/09132Genomicunknown
ss202088390BUSHMAN|BUSHMAN-chr16-87430143fwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat02/16/1003/08/10132Genomicunknown
ss2274144901000GENOMES|pilot_1_YRI_9224173_chr16_87430144fwd/A/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat04/22/1004/22/10132Genomicunknown
ss244308403ILLUMINA|CVDSNP55v1_A_rs7187889rev/BC/Tattatgaagaatttcctattaatctgaagagggggaagccaacctcacccagatctacct06/10/1006/10/10132Genomicunknown
ss342437124NHLBI-ESP|ESP2500-chr16-88902643byFreqfwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat03/25/1109/05/14134Genomicunknown
ss479223136ILLUMINA|HumanOmni1-Quad_v1-0_C_kgp16271451-0_B_R_1842895267fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc01/30/1208/28/15146Genomicunknown
ss481069647ILLUMINA|HumanOmni2.5-4v1_D_kgp16271451-0_B_R_1842895267fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc01/30/1210/27/16137Genomicunknown
ss483587128ILLUMINA|HumanOmni2.5-4v1_B_SNP16-87430144-0_B_R_1631394934fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc01/30/1210/28/16137Genomicunknown
ss4911102191000GENOMES|20110521_exome_618017_chr16_88902643fwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat02/10/1202/22/12137Genomicunknown
ss491513292EXOME_CHIP|nonsyn_229518_chr_16_88902643fwd/TA/Gaggtagatctgggtgaggttggcttccccctcttcagattaataggaaattcttcataat03/05/1203/05/12137Genomicunknown
ss534112743ILLUMINA|HumanOmni5-4v1_B_kgp16271451-0_B_R_1842895267fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc06/22/1208/29/15146Genomicunknown
ss565106045TISHKOFF|snp_chr16_88902643fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc11/22/1211/23/12138Genomicunknown
ss779252580ILLUMINA|HumanOmni25Exome-8v1_A_kgp16271451-0_B_R_1842895267fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/30/1307/10/15146Genomicunknown
ss781389047ILLUMINA|HumanOmni2.5-4v1_H_kgp16271451-0_B_R_1842895267fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/30/1307/29/15146Genomicunknown
ss783397958ILLUMINA|HumanOmniExpressExome-8v1_A_exm1269299-0_B_R_1921777818fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/31/1306/19/15146Genomicunknown
ss834719056ILLUMINA|HumanOmni2.5-8v1_A_kgp16271451-0_B_R_1842895267fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc09/18/1307/29/15146Genomicunknown
ss974496383JMKIDD_LAB|KhoeSan_Exomes_chr16_88902643fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc03/06/1403/06/14142Genomicunknown
ss1067565031JMKIDD_LAB|HGDP_exomes_chr16_88902643fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc07/09/1407/09/14142Genomicunknown
ss1080862746JMKIDD_LAB|HGDP_WGS_chr16_88902643fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc07/10/1407/12/14142Genomicunknown
ss13575146041000GENOMES|PHASE3_V1_70998778fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc08/16/1408/16/14142Genomicunknown
ss1635097026EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_16_88902643_39231611fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc03/04/1503/04/15144Genomicunknown
ss1678091059EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_16_88902643_39231611fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc03/04/1503/04/15144Genomicunknown
ss1692468240EVA_EXAC|EVA_EXAC_7816702fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc03/04/1503/04/15144Genomicunknown
ss1711440342EVA_MGP|EVA_XIMO_556102fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc03/09/1503/09/15144Genomicunknown
ss1752212380ILLUMINA|OmniExpressExome-8v1-1_B_exm1269299-0_B_R_1921777818fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/27/1506/09/15146Genomicunknown
ss1808658327HAMMER_LAB|Hsieh_7685347fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc07/15/1507/16/15146Genomicunknown
ss1917911566ILLUMINA|HumanExome-12v1-1_B_exm1269299-0_B_R_1921777818fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc10/16/1510/16/15147Genomicunknown
ss1936259799WEILL_CORNELL_DGM|SNV:chr16:88902643fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc10/16/1510/19/15147Genomicunknown
ss1946423668ILLUMINA|HumanCoreExome-12v1-0_C_exm1269299-0_B_R_1921777818fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc10/29/1510/29/15147Genomicunknown
ss1959710061ILLUMINA|exm1269299-0_B_R_1921777818fwd/TA/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc11/13/1511/13/15147Genomicunknown
ss2214729541HUMAN_LONGEVITY|HLI-16-88836235-G-Afwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc11/18/1611/18/16150Genomicunknown
ss2379552424TOPMED|16_88902643_G/Afwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc11/19/1611/19/16150Genomicunknown
ss2633361950ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp16271451-0_B_R_18428952fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc02/02/1702/02/17151Genomicunknown
ss2633361951ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs7187889-131_B_R_19085224fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc02/02/1702/02/17151Genomicunknown
ss2742240835GNOMAD|exomes_rs7187889fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/17/1705/17/17151Genomicunknown
ss2749624870GNOMAD|coding_rs7187889fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/17/1705/17/17151Genomicunknown
ss2946567563GNOMAD|rs7187889fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/23/1705/23/17151Genomicunknown
ss2985079765AFFY|Axiom_PsorMich_Affx-13430920fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/24/1705/24/17151Genomicunknown
ss3015022631SWEGEN|NC_000016.9:g.88902643G>Afwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc05/30/1705/30/17151Genomicunknown
ss3021740324ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm1269299-0_B_R_1921777818fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc06/28/1706/28/17151Genomicunknown
ss3254719904TOPMED|TOPMed_freeze_5?chr16:88,836,235fwd/A/Ggatctgggtgaggttggcttccccctcttcagattaataggaaattcttc10/01/1710/01/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs7187889|allelePos=201|totalLen=702|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CCGTCCCCAC GCGTCCCACG GGGCGAGGGT GATGAGGTCC CTGAACCCAT GCCTCCCACG
 GGGTGAGGTT GATGCATTCC TGTCCCCACG CCTCCCACAG GATGAGGTTG GTGCGGTCCC
 CGTCCCCATG CGTCCCACAG GGCGAGGATG GTGCGGTCCC CATCACCTGC AGGTAGATCT
 GGGTGAGGTT GGCTTCCCCC
 R
 TCTTCAGATT AATAGGAAAT TCTTCATAAT ATCTGAAAAG AACACAGATC CAGACAGACT
 TCAGAATTTA GGCCAAGAAA GTCCCGTTCT CCCTGATTTC ACCAGCAAAG CCATGGGCTT
 CATTTAAAAG AAGGCTAGgg ctgggcgtca tggctcatgc ctgtaatccc agcattttgg
 gaggctgagg aaggtggatc atgaggtcag gaatttgaga ccagcctggg caacatggtg
 aaactctgtc tctactaaaa atacaaaaat tagctgggcg tggtggcgca cgcctgtaat
 cccagctact tgagaggctg aggcaggaga attgcttgaa cccaggaggc ggaggttgca
 gtgagccgag atcgcgccac tgcaatccac cctgggtgac agagcaagat cctgtctcaa
 gaaaaaaaaa aaaaaGGAAG CCTGGAAATG AAATGTCCAC TCAGGGAACA ACCAAGCTGG
 ACGCATCCCT CGCTCCCCCA G

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010542
dbSNP Blast Analysis
3D structure mapping
NP_000503  

  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
ss10811144HapMap-CEUEuropean 222IG 0.027027030.972972991.000000000.013513510.98648649
HapMap-HCBAsian 82IG 0.048780490.951219501.000000000.024390240.97560978
HapMap-JPTAsian 164IG 0.073170730.926829281.000000000.036585360.96341461
HapMap-YRISub-Saharan African 212IG0.037735850.320754710.641509411.000000000.198113200.80188680
HAPMAP-ASW 96IG0.020833330.250000000.729166691.000000000.145833330.85416669
HAPMAP-CHBAsian 80IG 1.00000000 1.00000000
HAPMAP-CHD 164IG 0.012195120.987804891.000000000.006097560.99390244
HAPMAP-GIH 172IG 0.034883720.965116261.000000000.017441860.98255813
HAPMAP-LWK 174IG0.011494250.287356320.701149400.371093000.155172410.84482759
HAPMAP-MKK 284IG 0.063380280.936619701.000000000.031690140.96830988
HAPMAP-TSI 170IG 0.035294120.964705881.000000000.017647060.98235291
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss1357514604EAS 1008AF 1.00000000
EUR 1006AF 0.002000000.99799997
AFR 1322AF 0.156600000.84340006
AMR 694AF 0.015900000.98409998
SAS 978AF 1.00000000
ss1692468240ExAc_Aggregated_Populations121412AF 0.013408890.98659110
ss202088390BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss227414490pilot_1_YRI_low_coverage_panel 118AF 0.177966100.82203388
ss342437124ESP_Cohort_Populations 4550GF0.006153850.111648350.882197800.099721000.061978020.93802196
ss48417370AGI_ASP populationmultiple 68IG 0.117647060.882352951.000000000.058823530.94117647
ss69355253HapMap-CEUEuropean 120IG 1.00000000 1.00000000
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG0.016666670.283333330.699999990.654721000.158333330.84166664

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.027+/-0.1140000

  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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