rs6551640

Organism: Homo sapiens

Alleles: T>A

Gene : Feature

ADGRL3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0356 (10627/29782,GnomAD)
A=0324 (9459/29118,TOPMED)
A=0262 (1314/5008,1000G)
T==0496 (1911/3854,ALSPAC)
A=0492 (1823/3708,TWINSUK)

Position: chr4:61653103 (GRCh38.p7) (4q13.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 15 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.61653103T>A
GRCh37.p13 chr 4	NC_000004.11:g.62518821T>A
ADGRL3 RefSeqGene	NG_033950.2:g.456848T>A

Gene: ADGRL3, adhesion G protein-coupled receptor L3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ADGRL3 transcript variant 3	NM_001322246.1:c.	N/A	Intron Variant
ADGRL3 transcript variant 1	NM_001322402.1:c.	N/A	Intron Variant
ADGRL3 transcript variant 2	NM_015236.5:c.	N/A	Intron Variant
ADGRL3 transcript variant X4	XM_011531788.2:c.	N/A	Intron Variant
ADGRL3 transcript variant X11	XM_011531791.2:c.	N/A	Intron Variant
ADGRL3 transcript variant X1	XM_017007929.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X2	XM_017007930.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X3	XM_017007931.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X5	XM_017007932.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X6	XM_017007933.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X7	XM_017007934.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X8	XM_017007935.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X9	XM_017007936.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X10	XM_017007937.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X12	XM_017007938.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X13	XM_017007939.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X14	XM_017007940.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X15	XM_017007941.1:c.	N/A	Intron Variant
ADGRL3 transcript variant X16	XM_017007942.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.848	A=0.152
1000Genomes	American	Sub	694	T=0.670	A=0.330
1000Genomes	East Asian	Sub	1008	T=0.940	A=0.060
1000Genomes	Europe	Sub	1006	T=0.547	A=0.453
1000Genomes	Global	Study-wide	5008	T=0.738	A=0.262
1000Genomes	South Asian	Sub	978	T=0.620	A=0.380
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.496	A=0.504
The Genome Aggregation Database	African	Sub	8680	T=0.812	A=0.188
The Genome Aggregation Database	American	Sub	832	T=0.710	A=0.290
The Genome Aggregation Database	East Asian	Sub	1612	T=0.935	A=0.065
The Genome Aggregation Database	Europe	Sub	18356	T=0.537	A=0.462
The Genome Aggregation Database	Global	Study-wide	29782	T=0.643	A=0.356
The Genome Aggregation Database	Other	Sub	302	T=0.510	A=0.490
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.675	A=0.324
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.508	A=0.492

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs6551640	9.59E-06	alcohol and nictotine co-dependence	20158304

eQTL of rs6551640 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 rs6551640 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 )
chr4	62522037	62522202	E067	3216
chr4	62522037	62522202	E068	3216
chr4	62522631	62522759	E068	3810
chr4	62522037	62522202	E069	3216
chr4	62522037	62522202	E071	3216
chr4	62522631	62522759	E071	3810
chr4	62524433	62524494	E071	5612
chr4	62522037	62522202	E072	3216
chr4	62522631	62522759	E072	3810
chr4	62473862	62474047	E073	-44774
chr4	62521550	62521604	E074	2729
chr4	62522037	62522202	E074	3216
chr4	62522631	62522759	E074	3810
chr4	62496330	62496406	E081	-22415
chr4	62496474	62496539	E081	-22282