rs2407405

Homo sapiens
C>T
ARL15 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0370 (11064/29892,GnomAD)
C==0396 (11535/29118,TOPMED)
C==0453 (2269/5008,1000G)
C==0314 (1209/3854,ALSPAC)
C==0311 (1152/3708,TWINSUK)
chr5:54241716 (GRCh38.p7) (5q11.2)
AD
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
1 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.54241716C>T
GRCh37.p13 chr 5NC_000005.9:g.53537546C>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
1000GenomesAfricanSub1322C=0.500T=0.500
1000GenomesAmericanSub694C=0.540T=0.460
1000GenomesEast AsianSub1008C=0.572T=0.428
1000GenomesEuropeSub1006C=0.311T=0.689
1000GenomesGlobalStudy-wide5008C=0.453T=0.547
1000GenomesSouth AsianSub978C=0.350T=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.314T=0.686
The Genome Aggregation DatabaseAfricanSub8698C=0.466T=0.534
The Genome Aggregation DatabaseAmericanSub828C=0.520T=0.480
The Genome Aggregation DatabaseEast AsianSub1608C=0.606T=0.394
The Genome Aggregation DatabaseEuropeSub18456C=0.299T=0.700
The Genome Aggregation DatabaseGlobalStudy-wide29892C=0.370T=0.629
The Genome Aggregation DatabaseOtherSub302C=0.240T=0.760
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.396T=0.603
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.311T=0.689
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
rs24074054.69E-07alcohol dependence (age at onset)24962325

eQTL of rs2407405 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 rs2407405 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 )
chr55352492153525456E068-12090
chr55357394153574185E06936395
chr55357422253574433E06936676
chr55351066653510874E070-26672
chr55351115053511650E070-25896
chr55351327153513323E070-24223
chr55357394153574185E07236395
chr55357422253574433E07236676
chr55357444553574505E07236899
chr55357422253574433E07436676
chr55357444553574505E07436899
chr55351066653510874E081-26672
chr55351115053511650E081-25896
chr55351115053511650E082-25896







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr55355060653550896E07113060