rs6944759

Homo sapiens
C>T
GATAD1 : Intron Variant
PEX1 : 500B Downstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0040 (1208/29964,GnomAD)
T=0044 (1287/29118,TOPMED)
T=0091 (455/5008,1000G)
T=0017 (64/3854,ALSPAC)
T=0019 (70/3708,TWINSUK)
chr7:92486787 (GRCh38.p7) (7q21.2)
AD
GWASdb2
1   publication(s)
See rs on genome
37 Enhancers around
30 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.92486787C>T
GRCh37.p13 chr 7NC_000007.13:g.92116101C>T
PEX1 RefSeqGeneNG_008341.1:g.46745G>A

Gene: GATAD1, GATA zinc finger domain containing 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GATAD1 transcript variant 1NM_021167.4:c.N/AGenic Downstream Transcript Variant
GATAD1 transcript variant 2NR_052016.1:n.N/AGenic Downstream Transcript Variant
GATAD1 transcript variant X1XR_001744842.1:n.N/AIntron Variant
GATAD1 transcript variant X2XR_001744843.1:n.N/AIntron Variant
GATAD1 transcript variant X3XR_927494.2:n.N/AIntron Variant
GATAD1 transcript variant X4XR_927500.2:n.N/AIntron Variant
GATAD1 transcript variant X5XR_927503.2:n.N/AIntron Variant

Gene: PEX1, peroxisomal biogenesis factor 1(minus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
PEX1 transcript variant 1NM_000466.2:c.N/ADownstream Transcript Variant
PEX1 transcript variant 2NM_001282677.1:c.N/ADownstream Transcript Variant
PEX1 transcript variant 3NM_001282678.1:c.N/ADownstream Transcript Variant
PEX1 transcript variant X2XM_017012319.1:c.N/ADownstream Transcript Variant
PEX1 transcript variant X3XR_001744808.1:n.N/ADownstream Transcript Variant
PEX1 transcript variant X1XR_242246.4:n.N/ADownstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.959T=0.041
1000GenomesAmericanSub694C=0.900T=0.100
1000GenomesEast AsianSub1008C=0.719T=0.281
1000GenomesEuropeSub1006C=0.981T=0.019
1000GenomesGlobalStudy-wide5008C=0.909T=0.091
1000GenomesSouth AsianSub978C=0.970T=0.030
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.983T=0.017
The Genome Aggregation DatabaseAfricanSub8726C=0.962T=0.038
The Genome Aggregation DatabaseAmericanSub838C=0.870T=0.130
The Genome Aggregation DatabaseEast AsianSub1612C=0.704T=0.296
The Genome Aggregation DatabaseEuropeSub18486C=0.985T=0.014
The Genome Aggregation DatabaseGlobalStudy-wide29964C=0.959T=0.040
The Genome Aggregation DatabaseOtherSub302C=0.920T=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.955T=0.044
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.981T=0.019
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs69447590.00065alcohol dependence20201924

eQTL of rs6944759 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr7:92116101RBM48ENSG00000127993.10C>T2.2782e-4-41986Hypothalamus

meQTL of rs6944759 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 )
chr79207844092078538E067-37563
chr79207855092078697E067-37404
chr79208159592081651E067-34450
chr79216383492163874E06747733
chr79216392392164003E06747822
chr79216404892164147E06747947
chr79216480392164887E06748702
chr79215522792155275E06839126
chr79215528792155347E06839186
chr79216383492163874E06947733
chr79216392392164003E06947822
chr79216404892164147E06947947
chr79216480392164887E06948702
chr79216553392165573E06949432
chr79215484092154904E07038739
chr79215522792155275E07039126
chr79215528792155347E07039186
chr79215542692155482E07039325
chr79215522792155275E07139126
chr79215528792155347E07139186
chr79215542692155482E07139325
chr79207941892079493E072-36608
chr79215522792155275E07239126
chr79215528792155347E07239186
chr79215542692155482E07239325
chr79216392392164003E07247822
chr79216404892164147E07247947
chr79215522792155275E07339126
chr79215528792155347E07339186
chr79215542692155482E07339325
chr79207844092078538E074-37563
chr79207855092078697E074-37404
chr79216383492163874E07447733
chr79216392392164003E07447822
chr79216404892164147E07447947
chr79207844092078538E082-37563
chr79207855092078697E082-37404









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr79207636692078352E067-37749
chr79215674592158674E06740644
chr79215872192158793E06742620
chr79207636692078352E068-37749
chr79215674592158674E06840644
chr79215872192158793E06842620
chr79207636692078352E069-37749
chr79215674592158674E06940644
chr79215872192158793E06942620
chr79207636692078352E070-37749
chr79215674592158674E07040644
chr79215872192158793E07042620
chr79207636692078352E071-37749
chr79215674592158674E07140644
chr79215872192158793E07142620
chr79207636692078352E072-37749
chr79215674592158674E07240644
chr79215872192158793E07242620
chr79207636692078352E073-37749
chr79215674592158674E07340644
chr79215872192158793E07342620
chr79207636692078352E074-37749
chr79215674592158674E07440644
chr79215872192158793E07442620
chr79207636692078352E081-37749
chr79215674592158674E08140644
chr79215872192158793E08142620
chr79207636692078352E082-37749
chr79215674592158674E08240644
chr79215872192158793E08242620