rs12639304

Homo sapiens
A>T
TF : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0418 (12501/29902,GnomAD)
T=0465 (13543/29118,TOPMED)
T=0489 (2449/5008,1000G)
T=0335 (1290/3854,ALSPAC)
T=0319 (1183/3708,TWINSUK)
chr3:133722750 (GRCh38.p7) (3q22.1)
AD
GWASdb2
1   publication(s)
See rs on genome
74 Enhancers around
60 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.133722750A>T
GRCh37.p13 chr 3NC_000003.11:g.133441594A>T

Gene: TF, transferrin(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TF transcript variant 1NM_001063.3:c.N/AGenic Upstream Transcript Variant
TF transcript variant X1XM_017007089.1:c.N/AIntron Variant
TF transcript variant X2XM_017007090.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.374T=0.626
1000GenomesAmericanSub694A=0.570T=0.430
1000GenomesEast AsianSub1008A=0.530T=0.470
1000GenomesEuropeSub1006A=0.667T=0.333
1000GenomesGlobalStudy-wide5008A=0.511T=0.489
1000GenomesSouth AsianSub978A=0.480T=0.520
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.665T=0.335
The Genome Aggregation DatabaseAfricanSub8710A=0.395T=0.605
The Genome Aggregation DatabaseAmericanSub838A=0.510T=0.490
The Genome Aggregation DatabaseEast AsianSub1606A=0.551T=0.449
The Genome Aggregation DatabaseEuropeSub18448A=0.673T=0.326
The Genome Aggregation DatabaseGlobalStudy-wide29902A=0.581T=0.418
The Genome Aggregation DatabaseOtherSub300A=0.740T=0.260
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.534T=0.465
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.681T=0.319
PMID Title Author Journal
21665994Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.Kutalik ZHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs126393043.81E-12alcohol consumption21665994

eQTL of rs12639304 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 rs12639304 in Fetal Brain

Probe ID Position Gene beta p-value
cg01448562chr3:133502909-0.04887198538253041.4183e-16
cg16275903chr3:133524006SRPRB0.04901608066331357.9473e-16
cg08048268chr3:133502702-0.1073065882398992.0431e-15
cg08439880chr3:133502540-0.05978819357090382.2812e-13
cg16414030chr3:133502952-0.06779362665809884.4828e-13
cg11941060chr3:133502564-0.05024582881564534.5675e-11
cg20276088chr3:133502917-0.02594911950762194.9804e-10

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 )
chr3133395447133395540E067-46054
chr3133431016133431089E067-10505
chr3133436424133436504E067-5090
chr3133461397133461916E06719803
chr3133461945133462055E06720351
chr3133464069133464119E06722475
chr3133464448133464526E06722854
chr3133482923133483028E06741329
chr3133483054133483594E06741460
chr3133483998133484070E06742404
chr3133436424133436504E068-5090
chr3133464069133464119E06822475
chr3133482562133482616E06840968
chr3133482923133483028E06841329
chr3133483054133483594E06841460
chr3133431016133431089E069-10505
chr3133436424133436504E069-5090
chr3133461397133461916E06919803
chr3133461945133462055E06920351
chr3133464069133464119E06922475
chr3133473014133473073E06931420
chr3133473315133473659E06931721
chr3133476260133476458E06934666
chr3133482562133482616E06940968
chr3133482923133483028E06941329
chr3133483054133483594E06941460
chr3133483998133484070E06942404
chr3133484337133484387E06942743
chr3133482923133483028E07041329
chr3133483054133483594E07041460
chr3133395447133395540E071-46054
chr3133395561133395628E071-45966
chr3133431016133431089E071-10505
chr3133436424133436504E071-5090
chr3133461397133461916E07119803
chr3133461945133462055E07120351
chr3133464069133464119E07122475
chr3133473014133473073E07131420
chr3133473315133473659E07131721
chr3133482562133482616E07140968
chr3133482923133483028E07141329
chr3133483054133483594E07141460
chr3133483998133484070E07142404
chr3133484337133484387E07142743
chr3133431016133431089E072-10505
chr3133461397133461916E07219803
chr3133461945133462055E07220351
chr3133464069133464119E07222475
chr3133464448133464526E07222854
chr3133473014133473073E07231420
chr3133482923133483028E07241329
chr3133483054133483594E07241460
chr3133483998133484070E07242404
chr3133484337133484387E07242743
chr3133436424133436504E073-5090
chr3133461397133461916E07319803
chr3133461945133462055E07320351
chr3133464448133464526E07322854
chr3133482923133483028E07341329
chr3133483054133483594E07341460
chr3133431016133431089E074-10505
chr3133436424133436504E074-5090
chr3133461397133461916E07419803
chr3133461945133462055E07420351
chr3133464069133464119E07422475
chr3133473014133473073E07431420
chr3133473315133473659E07431721
chr3133476260133476458E07434666
chr3133482562133482616E07440968
chr3133482923133483028E07441329
chr3133483054133483594E07441460
chr3133483998133484070E07442404
chr3133484337133484387E07442743
chr3133464448133464526E08222854









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3133392888133393030E067-48564
chr3133393091133393483E067-48111
chr3133393533133393598E067-47996
chr3133393653133393755E067-47839
chr3133464975133465152E06723381
chr3133465195133465439E06723601
chr3133465691133465761E06724097
chr3133468272133468322E06726678
chr3133392888133393030E068-48564
chr3133393091133393483E068-48111
chr3133393533133393598E068-47996
chr3133393653133393755E068-47839
chr3133464975133465152E06823381
chr3133465195133465439E06823601
chr3133465691133465761E06824097
chr3133468272133468322E06826678
chr3133392888133393030E069-48564
chr3133393091133393483E069-48111
chr3133393533133393598E069-47996
chr3133393653133393755E069-47839
chr3133464975133465152E06923381
chr3133465195133465439E06923601
chr3133465691133465761E06924097
chr3133468272133468322E06926678
chr3133465195133465439E07023601
chr3133393091133393483E071-48111
chr3133393533133393598E071-47996
chr3133393653133393755E071-47839
chr3133464975133465152E07123381
chr3133465195133465439E07123601
chr3133465691133465761E07124097
chr3133468272133468322E07126678
chr3133392888133393030E072-48564
chr3133393091133393483E072-48111
chr3133393533133393598E072-47996
chr3133393653133393755E072-47839
chr3133464975133465152E07223381
chr3133465195133465439E07223601
chr3133465691133465761E07224097
chr3133468272133468322E07226678
chr3133392888133393030E073-48564
chr3133393091133393483E073-48111
chr3133393533133393598E073-47996
chr3133393653133393755E073-47839
chr3133464975133465152E07323381
chr3133465195133465439E07323601
chr3133465691133465761E07324097
chr3133468272133468322E07326678
chr3133393091133393483E074-48111
chr3133393533133393598E074-47996
chr3133393653133393755E074-47839
chr3133464975133465152E07423381
chr3133465195133465439E07423601
chr3133465691133465761E07424097
chr3133468272133468322E07426678
chr3133464975133465152E08123381
chr3133393091133393483E082-48111
chr3133393533133393598E082-47996
chr3133464975133465152E08223381
chr3133465195133465439E08223601