rs502396

Homo sapiens
C>T
TYMS : Intron Variant
TYMSOS : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0460 (13788/29914,GnomAD)
T=0427 (12447/29118,TOPMED)
T=0400 (2002/5008,1000G)
C==0485 (1871/3854,ALSPAC)
C==0469 (1740/3708,TWINSUK)
chr18:659236 (GRCh38.p7) (18p11.32)
AD
GWASdb2
11   publication(s)
See rs on genome
155 Enhancers around
18 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 18NC_000018.10:g.659236C>T
GRCh37.p13 chr 18NC_000018.9:g.659236C>T
TYMS RefSeqGene LRG_783

Gene: TYMS, thymidylate synthetase(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TYMS transcriptNM_001071.2:c.N/AIntron Variant

Gene: TYMSOS, TYMS opposite strand(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
TYMSOS transcriptNM_001012716.2:c.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.710T=0.290
1000GenomesAmericanSub694C=0.450T=0.550
1000GenomesEast AsianSub1008C=0.727T=0.273
1000GenomesEuropeSub1006C=0.486T=0.514
1000GenomesGlobalStudy-wide5008C=0.600T=0.400
1000GenomesSouth AsianSub978C=0.550T=0.450
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.485T=0.515
The Genome Aggregation DatabaseAfricanSub8700C=0.687T=0.313
The Genome Aggregation DatabaseAmericanSub838C=0.440T=0.560
The Genome Aggregation DatabaseEast AsianSub1620C=0.739T=0.261
The Genome Aggregation DatabaseEuropeSub18454C=0.456T=0.543
The Genome Aggregation DatabaseGlobalStudy-wide29914C=0.539T=0.460
The Genome Aggregation DatabaseOtherSub302C=0.520T=0.480
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.572T=0.427
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.469T=0.531
PMID Title Author Journal
22903727Maternal and infant gene-folate interactions and the risk of neural tube defects.Etheredge AJAm J Med Genet A
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
25344837Relationships among folate, alcohol consumption, gene variants in one-carbon metabolism and p16INK4a methylation and expression in healthy breast tissues.Llanos AACarcinogenesis
19064578No association of single nucleotide polymorphisms in one-carbon metabolism genes with prostate cancer risk.Stevens VLCancer Epidemiol Biomarkers Prev
18098291Folate metabolism genes, vegetable intake and renal cancer risk in central Europe.Moore LEInt J Cancer
28043790Thymidylate synthase gene polymorphisms as important contributors affecting hepatocellular carcinoma prognosis.Wang XClin Res Hepatol Gastroenterol
19493349118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects.Shaw GMBMC Med Genet
21254358Nonsyndromic cleft lip and palate: CRISPLD genes and the folate gene pathway connection.Chiquet BTBirth Defects Res A Clin Mol Teratol
21254359Folate pathway and nonsyndromic cleft lip and palate.Blanton SHBirth Defects Res A Clin Mol Teratol
19190136Association of thymidylate synthase gene with endometrial cancer risk in a Chinese population.Xu WHCancer Epidemiol Biomarkers Prev
21146954Genes and abdominal aortic aneurysm.Hinterseher IAnn Vasc Surg

P-Value

SNP ID p-value Traits Study
rs5023960.000797alcohol dependence20201924

eQTL of rs502396 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 rs502396 in Fetal Brain

Probe ID Position Gene beta p-value
cg16112050chr18:713200ENOSF1-0.05448857457295044.1621e-14
cg20977660chr18:657672TYMS|C18orf560.02938877765387769.8923e-9

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 )
chr18623947624258E067-34978
chr18624259624403E067-34833
chr18624458624604E067-34632
chr18642822642937E067-16299
chr18644135644240E067-14996
chr18644464644815E067-14421
chr18650831651031E067-8205
chr18651535651585E067-7651
chr18652021652517E067-6719
chr18659360659484E067124
chr18677681677839E06718445
chr18678642678714E06719406
chr18678794678887E06719558
chr18678924678979E06719688
chr18678999679053E06719763
chr18686025687136E06726789
chr18687194687252E06727958
chr18687429687591E06728193
chr18623947624258E068-34978
chr18624259624403E068-34833
chr18624458624604E068-34632
chr18642822642937E068-16299
chr18652021652517E068-6719
chr18652706652746E068-6490
chr18677629677679E06818393
chr18677681677839E06818445
chr18686025687136E06826789
chr18687194687252E06827958
chr18706519706639E06847283
chr18706669706719E06847433
chr18623947624258E069-34978
chr18624259624403E069-34833
chr18624458624604E069-34632
chr18624881624963E069-34273
chr18629623629673E069-29563
chr18634461635079E069-24157
chr18642822642937E069-16299
chr18643845643980E069-15256
chr18644135644240E069-14996
chr18644464644815E069-14421
chr18652021652517E069-6719
chr18652590652704E069-6532
chr18659360659484E069124
chr18659491659627E069255
chr18659655659748E069419
chr18677629677679E06918393
chr18677681677839E06918445
chr18677876678394E06918640
chr18678642678714E06919406
chr18678794678887E06919558
chr18678924678979E06919688
chr18678999679053E06919763
chr18685781686023E06926545
chr18686025687136E06926789
chr18687194687252E06927958
chr18706519706639E06947283
chr18706669706719E06947433
chr18621268621904E070-37332
chr18624458624604E070-34632
chr18625399625491E070-33745
chr18625626626010E070-33226
chr18626373626492E070-32744
chr18634461635079E070-24157
chr18677876678394E07018640
chr18621268621904E071-37332
chr18623947624258E071-34978
chr18624259624403E071-34833
chr18624458624604E071-34632
chr18634461635079E071-24157
chr18642822642937E071-16299
chr18643845643980E071-15256
chr18644135644240E071-14996
chr18644464644815E071-14421
chr18650831651031E071-8205
chr18651535651585E071-7651
chr18652021652517E071-6719
chr18652590652704E071-6532
chr18652706652746E071-6490
chr18659360659484E071124
chr18677168677218E07117932
chr18677232677352E07117996
chr18677629677679E07118393
chr18677681677839E07118445
chr18677876678394E07118640
chr18678642678714E07119406
chr18678794678887E07119558
chr18685571685737E07126335
chr18685781686023E07126545
chr18686025687136E07126789
chr18687194687252E07127958
chr18687429687591E07128193
chr18623947624258E072-34978
chr18624259624403E072-34833
chr18624458624604E072-34632
chr18634461635079E072-24157
chr18642822642937E072-16299
chr18677168677218E07217932
chr18677232677352E07217996
chr18677629677679E07218393
chr18677681677839E07218445
chr18677876678394E07218640
chr18678642678714E07219406
chr18678794678887E07219558
chr18678924678979E07219688
chr18678999679053E07219763
chr18686025687136E07226789
chr18687194687252E07227958
chr18659360659484E073124
chr18677681677839E07318445
chr18677876678394E07318640
chr18678642678714E07319406
chr18678794678887E07319558
chr18678924678979E07319688
chr18678999679053E07319763
chr18685781686023E07326545
chr18686025687136E07326789
chr18687194687252E07327958
chr18687429687591E07328193
chr18624259624403E074-34833
chr18624458624604E074-34632
chr18642822642937E074-16299
chr18643845643980E074-15256
chr18644135644240E074-14996
chr18644464644815E074-14421
chr18652021652517E074-6719
chr18659360659484E074124
chr18659491659627E074255
chr18677232677352E07417996
chr18677876678394E07418640
chr18678642678714E07419406
chr18678794678887E07419558
chr18686025687136E07426789
chr18687194687252E07427958
chr18687429687591E07428193
chr18693844694232E07434608
chr18694285694555E07435049
chr18625399625491E081-33745
chr18678642678714E08119406
chr18678794678887E08119558
chr18678924678979E08119688
chr18678999679053E08119763
chr18679271679321E08120035
chr18679539679850E08120303
chr18679871679983E08120635
chr18680063680148E08120827
chr18680195680305E08120959
chr18680356680669E08121120
chr18693364693772E08134128
chr18693844694232E08134608
chr18677629677679E08218393
chr18677681677839E08218445
chr18678642678714E08219406
chr18678794678887E08219558
chr18678924678979E08219688
chr18678999679053E08219763










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr18656901657034E067-2202
chr18657153659104E067-132
chr18656709656802E068-2434
chr18656901657034E068-2202
chr18657153659104E068-132
chr18656709656802E069-2434
chr18656901657034E069-2202
chr18657153659104E069-132
chr18656901657034E070-2202
chr18657153659104E070-132
chr18657153659104E071-132
chr18657153659104E072-132
chr18656901657034E073-2202
chr18657153659104E073-132
chr18657153659104E074-132
chr18657153659104E081-132
chr18656901657034E082-2202
chr18657153659104E082-132