rs1800624

Homo sapiens
A>T
AGER : Non Coding Transcript Variant
PBX2 : 500B Downstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0200 (5976/29786,GnomAD)
T=0150 (749/5008,1000G)
T=0191 (737/3854,ALSPAC)
T=0215 (797/3708,TWINSUK)
chr6:32184610 (GRCh38.p7) (6p21.32)
AD
GWASdb2
30   publication(s)
See rs on genome
125 Enhancers around
96 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.32184610A>T
GRCh37.p13 chr 6NC_000006.11:g.32152387A>T
AGER RefSeqGeneNG_029868.1:g.4713T>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.3622962A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.3623068A>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.3500817T>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.3500115T>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.3407811A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.3413407A>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.3489591A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.3495211A>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.2:g.3517212A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.1:g.3467128A>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.3526629A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.3532214A>T

Gene: AGER, advanced glycosylation end product-specific receptor(minus strand)

Molecule type Change Amino acid[Codon] SO Term
AGER transcript variant 1NM_001136.4:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 2NM_001206929.1:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 3NM_001206932.1:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 4NM_001206934.1:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 5NM_001206936.1:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 6NM_001206940.1:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 8NM_001206954.1:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 9NM_001206966.1:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 7NM_172197.2:c.N/AGenic Upstream Transcript Variant
AGER transcript variant 10NR_038190.1:n.N/AGenic Upstream Transcript Variant
AGER transcript variant X1XM_017010328.1:c.N/A5 Prime UTR Variant
AGER transcript variant X2XR_001743189.1:n....XR_001743189.1:n.638T>AT>ANon Coding Transcript Variant
AGER transcript variant X3XR_001743190.1:n....XR_001743190.1:n.638T>AT>ANon Coding Transcript Variant

Gene: PBX2, pre-B-cell leukemia homeobox 2(minus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
PBX2 transcriptNM_002586.4:c.N/ADownstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.987T=0.013
1000GenomesAmericanSub694A=0.720T=0.280
1000GenomesEast AsianSub1008A=0.863T=0.137
1000GenomesEuropeSub1006A=0.750T=0.250
1000GenomesGlobalStudy-wide5008A=0.850T=0.150
1000GenomesSouth AsianSub978A=0.850T=0.150
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.809T=0.191
The Genome Aggregation DatabaseAfricanSub8590A=0.960T=0.040
The Genome Aggregation DatabaseAmericanSub836A=0.730T=0.270
The Genome Aggregation DatabaseEast AsianSub1608A=0.874T=0.126
The Genome Aggregation DatabaseEuropeSub18452A=0.723T=0.276
The Genome Aggregation DatabaseGlobalStudy-wide29786A=0.799T=0.200
The Genome Aggregation DatabaseOtherSub300A=0.690T=0.310
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.785T=0.215
PMID Title Author Journal
20353610Association analysis of ADPRT1, AKR1B1, RAGE, GFPT2 and PAI-1 gene polymorphisms with chronic renal insufficiency among Asian Indians with type-2 diabetes.Prasad PBMC Med Genet
27114872Association of the receptor for advanced glycation end-products (RAGE) gene polymorphisms in Malaysian patients with chronic kidney disease.Wong FNPeerJ
27730450Candidate gene studies of diabetic retinopathy in human.Priscakova PMol Biol Rep
27047454Genome-Wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis.Dix AFront Microbiol
22827914Identification of haplotype tag single nucleotide polymorphisms within the receptor for advanced glycation end products gene and their clinical relevance in patients with major trauma.Zeng LCrit Care
25379135Determinants of concentrations of N(epsilon)-carboxymethyl-lysine and soluble receptor for advanced glycation end products and their associations with risk of pancreatic cancer.Duan ZInt J Mol Epidemiol Genet
22879966Systematic testing of literature reported genetic variation associated with coronary restenosis: results of the GENDER Study.Verschuren JJPLoS One
27241711Genetic predisposition of six well-defined polymorphisms in HMGB1/RAGE pathway to breast cancer in a large Han Chinese population.Yue LJ Cell Mol Med
21254849AGER gene -374T>A (rs1800624) polymorphism is not associated with the severity of non-diabetic coronary artery disease in Han Chinese.Lu WClin Chem Lab Med
26456846Functional promoter polymorphisms of the receptor for advanced glycation end products in children and adolescents with type 1 diabetes.Gomes LCMol Cell Probes
27699858Genetic association between RAGE polymorphisms and Alzheimer's disease and Lewy body dementias in a Japanese cohort: a case-control study.Takeshita YInt J Geriatr Psychiatry
20051912The association between the -374T/A polymorphism of the receptor for advanced glycation endproducts gene and blood pressure and arterial stiffness is modified by glucose metabolism status: the Hoorn and CoDAM studies.Engelen LJ Hypertens
26313784Effects of RAGE Gene Polymorphisms on the Risk and Progression of Hepatocellular Carcinoma.Su SCMedicine (Baltimore)
24619131The relationship between RAGE gene four common polymorphisms and breast cancer risk in northeastern Han Chinese.Pan HSci Rep
26429324Receptor for advanced glycation end products (RAGE) gene polymorphism and cardiovascular disease in end-stage renal disease patients.Buraczynska MHum Immunol
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry
25407489Polymorphisms of the receptor for advanced glycation end-products and glyoxalase I in patients with renal cancer.Chocholaty MTumour Biol
21311028The functional -374T/A polymorphism of the receptor for advanced glycation end products may modulate Crohn's disease.Dabritz JAm J Physiol Gastrointest Liver Physiol
24605038RAGE gene three polymorphisms with Crohn's disease susceptibility in Chinese Han population.Wang ZTWorld J Gastroenterol
25991559Oxidative stress-related genes in type 2 diabetes: association analysis and their clinical impact.Haldar SRBiochem Genet
18575614Association between LTA, TNF and AGER polymorphisms and late diabetic complications.Lindholm EPLoS One
27277665Genetic risk factors for restenosis after percutaneous coronary intervention in Kazakh population.Zholdybayeva EVHum Genomics
23236395Meta-analysis of RAGE gene polymorphism and coronary heart disease risk.Wang JPLoS One
27746844Clinical Value of High Mobility Group Box 1 and the Receptor for Advanced Glycation End-products in Head and Neck Cancer: A Systematic Review.Nguyen AInt Arch Otorhinolaryngol
22133449Polymorphisms of the promoter and exon 3 of the receptor for advanced glycation end products (RAGE) in Euro- and Afro-Brazilians.Torres MCInt J Immunogenet
19587357A systematic meta-analysis of genetic association studies for diabetic retinopathy.Abhary SDiabetes
25582438RAGE gene polymorphism and environmental factor in the risk of oral cancer.Su SJ Dent Res
22964273Association study of polymorphisms in the receptor for advanced glycation end-products (RAGE) gene with susceptibility and prognosis of heart failure.Cohen CRGene
22114731Genetically-determined hyperfunction of the S100B/RAGE axis is a risk factor for aspergillosis in stem cell transplant recipients.Cunha CPLoS One
18796298Polymorphisms in advanced glycosylation end product-specific receptor (AGER) gene, insulin resistance, and type 2 diabetes mellitus.Goulart ACClin Chim Acta

P-Value

SNP ID p-value Traits Study
rs18006245.4E-05alcoholism (heaviness of drinking)21529783

eQTL of rs1800624 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs1800624 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr63213140432132029E067-20358
chr63213204232132473E067-19914
chr63213712732137260E067-15127
chr63213741432137579E067-14808
chr63214170332141762E067-10625
chr63214176932141842E067-10545
chr63214191632141966E067-10421
chr63214233532142389E067-9998
chr63215534932155418E0672962
chr63215553232155614E0673145
chr63215593232156067E0673545
chr63215610732156162E0673720
chr63216207032162425E0679683
chr63211461732114728E068-37659
chr63213119332131243E068-21144
chr63213140432132029E068-20358
chr63213204232132473E068-19914
chr63214037332141457E068-10930
chr63214233532142389E068-9998
chr63214762532147697E068-4690
chr63214774032147794E068-4593
chr63214791032147963E068-4424
chr63215078832150865E068-1522
chr63215100832151063E068-1324
chr63215114932151415E068-972
chr63215142332151546E068-841
chr63215155732151682E068-705
chr63215172232151814E068-573
chr63215448632154586E0682099
chr63215484532155067E0682458
chr63215514032155200E0682753
chr63215534932155418E0682962
chr63215553232155614E0683145
chr63215593232156067E0683545
chr63215610732156162E0683720
chr63216207032162425E0689683
chr63217130832171535E06818921
chr63213119332131243E069-21144
chr63213140432132029E069-20358
chr63213204232132473E069-19914
chr63214191632141966E069-10421
chr63214233532142389E069-9998
chr63215610732156162E0693720
chr63216207032162425E0699683
chr63212363332123686E070-28701
chr63214037332141457E070-10930
chr63214233532142389E070-9998
chr63214762532147697E070-4690
chr63214774032147794E070-4593
chr63214791032147963E070-4424
chr63214871032148806E070-3581
chr63214883932148935E070-3452
chr63214903932149094E070-3293
chr63214981132149900E070-2487
chr63214998332150129E070-2258
chr63215484532155067E0702458
chr63215514032155200E0702753
chr63215534932155418E0702962
chr63215925132159583E0706864
chr63215959732159659E0707210
chr63216195132162016E0709564
chr63216207032162425E0709683
chr63212363332123686E071-28701
chr63213119332131243E071-21144
chr63214762532147697E071-4690
chr63214774032147794E071-4593
chr63215484532155067E0712458
chr63215514032155200E0712753
chr63215534932155418E0712962
chr63215553232155614E0713145
chr63215593232156067E0713545
chr63215610732156162E0713720
chr63216207032162425E0719683
chr63213119332131243E072-21144
chr63213140432132029E072-20358
chr63213204232132473E072-19914
chr63214233532142389E072-9998
chr63215142332151546E072-841
chr63213140432132029E073-20358
chr63213204232132473E073-19914
chr63214037332141457E073-10930
chr63214170332141762E073-10625
chr63214176932141842E073-10545
chr63214191632141966E073-10421
chr63214233532142389E073-9998
chr63214762532147697E073-4690
chr63214774032147794E073-4593
chr63214791032147963E073-4424
chr63215484532155067E0732458
chr63215514032155200E0732753
chr63215534932155418E0732962
chr63215553232155614E0733145
chr63215593232156067E0733545
chr63215610732156162E0733720
chr63216207032162425E0739683
chr63213119332131243E074-21144
chr63213140432132029E074-20358
chr63213204232132473E074-19914
chr63214233532142389E074-9998
chr63216207032162425E0749683
chr63210478932104834E081-47553
chr63212363332123686E081-28701
chr63214762532147697E081-4690
chr63214774032147794E081-4593
chr63214791032147963E081-4424
chr63215345232153509E0811065
chr63215351132153766E0811124
chr63215925132159583E0816864
chr63215959732159659E0817210
chr63216195132162016E0819564
chr63216207032162425E0819683
chr63212363332123686E082-28701
chr63214037332141457E082-10930
chr63214791032147963E082-4424
chr63214871032148806E082-3581
chr63214883932148935E082-3452
chr63214903932149094E082-3293
chr63215448632154586E0822099
chr63215484532155067E0822458
chr63215514032155200E0822753
chr63215534932155418E0822962
chr63215553232155614E0823145
chr63215593232156067E0823545
chr63216195132162016E0829564
chr63216207032162425E0829683










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63211774032118318E067-34069
chr63211832632118549E067-33838
chr63211863132118770E067-33617
chr63212072732122781E067-29606
chr63214303232146367E067-6020
chr63214639832146872E067-5515
chr63215755932157851E0675172
chr63215790332159054E0675516
chr63215968032160003E0677293
chr63216265032165555E06710263
chr63211774032118318E068-34069
chr63211832632118549E068-33838
chr63211863132118770E068-33617
chr63212072732122781E068-29606
chr63214303232146367E068-6020
chr63214639832146872E068-5515
chr63215755932157851E0685172
chr63215790332159054E0685516
chr63215968032160003E0687293
chr63216265032165555E06810263
chr63211774032118318E069-34069
chr63211832632118549E069-33838
chr63211863132118770E069-33617
chr63212072732122781E069-29606
chr63214303232146367E069-6020
chr63214639832146872E069-5515
chr63215755932157851E0695172
chr63215790332159054E0695516
chr63215968032160003E0697293
chr63216265032165555E06910263
chr63211595432116004E070-36383
chr63211608332116139E070-36248
chr63211706932117119E070-35268
chr63211774032118318E070-34069
chr63211832632118549E070-33838
chr63211863132118770E070-33617
chr63212072732122781E070-29606
chr63214303232146367E070-6020
chr63214639832146872E070-5515
chr63215755932157851E0705172
chr63215790332159054E0705516
chr63216265032165555E07010263
chr63211617932116987E071-35400
chr63211774032118318E071-34069
chr63211832632118549E071-33838
chr63211863132118770E071-33617
chr63212072732122781E071-29606
chr63214303232146367E071-6020
chr63214639832146872E071-5515
chr63215755932157851E0715172
chr63215790332159054E0715516
chr63215968032160003E0717293
chr63216265032165555E07110263
chr63211706932117119E072-35268
chr63211774032118318E072-34069
chr63211832632118549E072-33838
chr63211863132118770E072-33617
chr63212072732122781E072-29606
chr63214303232146367E072-6020
chr63214639832146872E072-5515
chr63215755932157851E0725172
chr63215790332159054E0725516
chr63216265032165555E07210263
chr63211774032118318E073-34069
chr63211832632118549E073-33838
chr63211863132118770E073-33617
chr63212072732122781E073-29606
chr63214303232146367E073-6020
chr63214639832146872E073-5515
chr63215755932157851E0735172
chr63215790332159054E0735516
chr63216265032165555E07310263
chr63211863132118770E074-33617
chr63212072732122781E074-29606
chr63214303232146367E074-6020
chr63214639832146872E074-5515
chr63215755932157851E0745172
chr63215790332159054E0745516
chr63216265032165555E07410263
chr63212072732122781E081-29606
chr63214303232146367E081-6020
chr63214639832146872E081-5515
chr63216265032165555E08110263
chr63211595432116004E082-36383
chr63211608332116139E082-36248
chr63211617932116987E082-35400
chr63211706932117119E082-35268
chr63211774032118318E082-34069
chr63211832632118549E082-33838
chr63211863132118770E082-33617
chr63212072732122781E082-29606
chr63214303232146367E082-6020
chr63214639832146872E082-5515
chr63215755932157851E0825172
chr63215790332159054E0825516
chr63216265032165555E08210263