SNP Detail Info-rs6872062

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ARL15 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0371 (11107/29864,GnomAD)
G==0398 (11616/29118,TOPMED)
G==0456 (2286/5008,1000G)
G==0313 (1208/3854,ALSPAC)
G==0310 (1149/3708,TWINSUK)

Position: chr5:54245723 (GRCh38.p7) (5q11.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 15 Enhancers around

Promoter: 1 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.54245723G>A
GRCh37.p13 chr 5	NC_000005.9:g.53541553G>A

Molecule type	Change	Amino acid[Codon]	SO Term
ARL15 transcript	NM_019087.2:c.	N/A	Intron Variant
ARL15 transcript variant X1	XM_011543498.2:c.	N/A	Intron Variant
ARL15 transcript variant X2	XM_011543499.2:c.	N/A	Intron Variant
ARL15 transcript variant X3	XM_011543500.2:c.	N/A	Intron Variant
ARL15 transcript variant X4	XM_017009598.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.511	A=0.489
1000Genomes	American	Sub	694	G=0.540	A=0.460
1000Genomes	East Asian	Sub	1008	G=0.573	A=0.427
1000Genomes	Europe	Sub	1006	G=0.309	A=0.691
1000Genomes	Global	Study-wide	5008	G=0.456	A=0.544
1000Genomes	South Asian	Sub	978	G=0.350	A=0.650
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.313	A=0.687
The Genome Aggregation Database	African	Sub	8692	G=0.471	A=0.529
The Genome Aggregation Database	American	Sub	836	G=0.520	A=0.480
The Genome Aggregation Database	East Asian	Sub	1620	G=0.604	A=0.396
The Genome Aggregation Database	Europe	Sub	18414	G=0.300	A=0.700
The Genome Aggregation Database	Global	Study-wide	29864	G=0.371	A=0.628
The Genome Aggregation Database	Other	Sub	302	G=0.240	A=0.760
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.398	A=0.601
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.310	A=0.690

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

SNP ID	p-value	Traits	Study
rs6872062	7.83E-07	alcohol dependence (age at onset)	24962325

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr5	53524921	53525456	E068	-16097
chr5	53573941	53574185	E069	32388
chr5	53574222	53574433	E069	32669
chr5	53510666	53510874	E070	-30679
chr5	53511150	53511650	E070	-29903
chr5	53513271	53513323	E070	-28230
chr5	53573941	53574185	E072	32388
chr5	53574222	53574433	E072	32669
chr5	53574445	53574505	E072	32892
chr5	53574222	53574433	E074	32669
chr5	53574445	53574505	E074	32892
chr5	53591192	53591246	E074	49639
chr5	53510666	53510874	E081	-30679
chr5	53511150	53511650	E081	-29903
chr5	53511150	53511650	E082	-29903

rs6872062