rs7725454

Homo sapiens
A>T
ARL15 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0382 (11443/29914,GnomAD)
A==0414 (12063/29118,TOPMED)
A==0463 (2319/5008,1000G)
A==0314 (1211/3854,ALSPAC)
A==0310 (1150/3708,TWINSUK)
chr5:54286570 (GRCh38.p7) (5q11.2)
AD
GWASdb2
1   publication(s)
See rs on genome
26 Enhancers around
11 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.54286570A>T
GRCh37.p13 chr 5NC_000005.9:g.53582400A>T

Gene: ARL15, ADP ribosylation factor like GTPase 15(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ARL15 transcriptNM_019087.2:c.N/AIntron Variant
ARL15 transcript variant X1XM_011543498.2:c.N/AIntron Variant
ARL15 transcript variant X2XM_011543499.2:c.N/AIntron Variant
ARL15 transcript variant X3XM_011543500.2:c.N/AIntron Variant
ARL15 transcript variant X4XM_017009598.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.524T=0.476
1000GenomesAmericanSub694A=0.540T=0.460
1000GenomesEast AsianSub1008A=0.577T=0.423
1000GenomesEuropeSub1006A=0.317T=0.683
1000GenomesGlobalStudy-wide5008A=0.463T=0.537
1000GenomesSouth AsianSub978A=0.360T=0.640
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.314T=0.686
The Genome Aggregation DatabaseAfricanSub8692A=0.501T=0.499
The Genome Aggregation DatabaseAmericanSub830A=0.530T=0.470
The Genome Aggregation DatabaseEast AsianSub1618A=0.610T=0.390
The Genome Aggregation DatabaseEuropeSub18474A=0.302T=0.697
The Genome Aggregation DatabaseGlobalStudy-wide29914A=0.382T=0.617
The Genome Aggregation DatabaseOtherSub300A=0.240T=0.760
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.414T=0.585
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.310T=0.690
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs77254549.42E-07alcohol dependence (age at onset)24962325

eQTL of rs7725454 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 rs7725454 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 )
chr55359219153592302E0679791
chr55359230553592489E0679905
chr55360474653604828E06722346
chr55359156353591979E0689163
chr55359219153592302E0689791
chr55359230553592489E0689905
chr55357394153574185E069-8215
chr55357422253574433E069-7967
chr55360335753603465E07020957
chr55360351753603786E07021117
chr55360440353604546E07022003
chr55360474653604828E07122346
chr55357394153574185E072-8215
chr55357422253574433E072-7967
chr55357444553574505E072-7895
chr55357422253574433E074-7967
chr55357444553574505E074-7895
chr55359119253591246E0748792
chr55359156353591979E0749163
chr55359219153592302E0749791
chr55359230553592489E0749905
chr55360351753603786E08121117
chr55360427953604329E08121879
chr55360440353604546E08122003
chr55360474653604828E08122346
chr55360803253608085E08125632








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr55360503053607991E06722630
chr55360503053607991E06822630
chr55360503053607991E06922630
chr55360503053607991E07022630
chr55355060653550896E071-31504
chr55360503053607991E07122630
chr55360503053607991E07222630
chr55360503053607991E07322630
chr55360503053607991E07422630
chr55360503053607991E08122630
chr55360503053607991E08222630