rs6747728

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

GPR55 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0329 (9874/29940,GnomAD)
G=0398 (11602/29118,TOPMED)
G=0374 (1872/5008,1000G)
G=0215 (830/3854,ALSPAC)
G=0242 (898/3708,TWINSUK)

Position: chr2:230914061 (GRCh38.p7) (2q37.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 176 Enhancers around

Promoter: 27 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.230914061A>G
GRCh37.p13 chr 2	NC_000002.11:g.231778776A>G

Gene: GPR55, G protein-coupled receptor 55(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GPR55 transcript	NM_005683.3:c.	N/A	Intron Variant
GPR55 transcript variant X1	XM_005246952.3:c.	N/A	Intron Variant
GPR55 transcript variant X2	XM_011512175.2:c.	N/A	Intron Variant
GPR55 transcript variant X3	XM_011512176.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.335	G=0.665
1000Genomes	American	Sub	694	A=0.790	G=0.210
1000Genomes	East Asian	Sub	1008	A=0.759	G=0.241
1000Genomes	Europe	Sub	1006	A=0.780	G=0.220
1000Genomes	Global	Study-wide	5008	A=0.626	G=0.374
1000Genomes	South Asian	Sub	978	A=0.610	G=0.390
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.785	G=0.215
The Genome Aggregation Database	African	Sub	8710	A=0.419	G=0.581
The Genome Aggregation Database	American	Sub	836	A=0.830	G=0.170
The Genome Aggregation Database	East Asian	Sub	1618	A=0.800	G=0.200
The Genome Aggregation Database	Europe	Sub	18474	A=0.769	G=0.231
The Genome Aggregation Database	Global	Study-wide	29940	A=0.670	G=0.329
The Genome Aggregation Database	Other	Sub	302	A=0.730	G=0.270
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.601	G=0.398
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.758	G=0.242

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs6747728	0.00092	alcohol dependence	20201924

eQTL of rs6747728 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 rs6747728 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 )
chr2	231732667	231732755	E067	-46021
chr2	231732859	231736064	E067	-42712
chr2	231736094	231736282	E067	-42494
chr2	231736314	231736388	E067	-42388
chr2	231736559	231737141	E067	-41635
chr2	231737257	231737393	E067	-41383
chr2	231737800	231737985	E067	-40791
chr2	231750597	231750805	E067	-27971
chr2	231750876	231751053	E067	-27723
chr2	231751146	231751217	E067	-27559
chr2	231751503	231751574	E067	-27202
chr2	231751596	231751771	E067	-27005
chr2	231758116	231758203	E067	-20573
chr2	231758218	231758310	E067	-20466
chr2	231764041	231764219	E067	-14557
chr2	231764378	231764430	E067	-14346
chr2	231796611	231797053	E067	17835
chr2	231797299	231797732	E067	18523
chr2	231732667	231732755	E068	-46021
chr2	231732859	231736064	E068	-42712
chr2	231736094	231736282	E068	-42494
chr2	231736314	231736388	E068	-42388
chr2	231736559	231737141	E068	-41635
chr2	231737257	231737393	E068	-41383
chr2	231737800	231737985	E068	-40791
chr2	231742251	231743115	E068	-35661
chr2	231743155	231743215	E068	-35561
chr2	231743408	231743484	E068	-35292
chr2	231743576	231743665	E068	-35111
chr2	231750200	231750303	E068	-28473
chr2	231754968	231755243	E068	-23533
chr2	231755358	231755565	E068	-23211
chr2	231755852	231755939	E068	-22837
chr2	231755982	231756084	E068	-22692
chr2	231758116	231758203	E068	-20573
chr2	231758218	231758310	E068	-20466
chr2	231758547	231758933	E068	-19843
chr2	231758970	231759400	E068	-19376
chr2	231764041	231764219	E068	-14557
chr2	231764378	231764430	E068	-14346
chr2	231765153	231765208	E068	-13568
chr2	231772969	231773023	E068	-5753
chr2	231773054	231773221	E068	-5555
chr2	231797299	231797732	E068	18523
chr2	231823297	231823360	E068	44521
chr2	231732667	231732755	E069	-46021
chr2	231732859	231736064	E069	-42712
chr2	231736094	231736282	E069	-42494
chr2	231736314	231736388	E069	-42388
chr2	231736559	231737141	E069	-41635
chr2	231737257	231737393	E069	-41383
chr2	231737800	231737985	E069	-40791
chr2	231750597	231750805	E069	-27971
chr2	231750876	231751053	E069	-27723
chr2	231751071	231751121	E069	-27655
chr2	231751146	231751217	E069	-27559
chr2	231751503	231751574	E069	-27202
chr2	231751596	231751771	E069	-27005
chr2	231754968	231755243	E069	-23533
chr2	231755358	231755565	E069	-23211
chr2	231758116	231758203	E069	-20573
chr2	231758970	231759400	E069	-19376
chr2	231764041	231764219	E069	-14557
chr2	231764378	231764430	E069	-14346
chr2	231732667	231732755	E070	-46021
chr2	231732859	231736064	E070	-42712
chr2	231736094	231736282	E070	-42494
chr2	231736314	231736388	E070	-42388
chr2	231750200	231750303	E070	-28473
chr2	231751503	231751574	E070	-27202
chr2	231751596	231751771	E070	-27005
chr2	231732859	231736064	E071	-42712
chr2	231736094	231736282	E071	-42494
chr2	231736314	231736388	E071	-42388
chr2	231736559	231737141	E071	-41635
chr2	231737257	231737393	E071	-41383
chr2	231750200	231750303	E071	-28473
chr2	231750597	231750805	E071	-27971
chr2	231750876	231751053	E071	-27723
chr2	231751071	231751121	E071	-27655
chr2	231751146	231751217	E071	-27559
chr2	231751503	231751574	E071	-27202
chr2	231751596	231751771	E071	-27005
chr2	231758116	231758203	E071	-20573
chr2	231758218	231758310	E071	-20466
chr2	231758547	231758933	E071	-19843
chr2	231758970	231759400	E071	-19376
chr2	231764041	231764219	E071	-14557
chr2	231764378	231764430	E071	-14346
chr2	231808137	231808208	E071	29361
chr2	231732667	231732755	E072	-46021
chr2	231732859	231736064	E072	-42712
chr2	231736094	231736282	E072	-42494
chr2	231736314	231736388	E072	-42388
chr2	231736559	231737141	E072	-41635
chr2	231737257	231737393	E072	-41383
chr2	231737800	231737985	E072	-40791
chr2	231743408	231743484	E072	-35292
chr2	231743576	231743665	E072	-35111
chr2	231743691	231743860	E072	-34916
chr2	231750200	231750303	E072	-28473
chr2	231750597	231750805	E072	-27971
chr2	231750876	231751053	E072	-27723
chr2	231751596	231751771	E072	-27005
chr2	231758116	231758203	E072	-20573
chr2	231758218	231758310	E072	-20466
chr2	231758547	231758933	E072	-19843
chr2	231758970	231759400	E072	-19376
chr2	231764041	231764219	E072	-14557
chr2	231764378	231764430	E072	-14346
chr2	231732667	231732755	E073	-46021
chr2	231732859	231736064	E073	-42712
chr2	231736094	231736282	E073	-42494
chr2	231736314	231736388	E073	-42388
chr2	231736559	231737141	E073	-41635
chr2	231737257	231737393	E073	-41383
chr2	231750597	231750805	E073	-27971
chr2	231758116	231758203	E073	-20573
chr2	231758218	231758310	E073	-20466
chr2	231758547	231758933	E073	-19843
chr2	231758970	231759400	E073	-19376
chr2	231764041	231764219	E073	-14557
chr2	231764378	231764430	E073	-14346
chr2	231796155	231796455	E073	17379
chr2	231823297	231823360	E073	44521
chr2	231732859	231736064	E074	-42712
chr2	231736094	231736282	E074	-42494
chr2	231736314	231736388	E074	-42388
chr2	231750597	231750805	E074	-27971
chr2	231750876	231751053	E074	-27723
chr2	231751071	231751121	E074	-27655
chr2	231751146	231751217	E074	-27559
chr2	231751503	231751574	E074	-27202
chr2	231751596	231751771	E074	-27005
chr2	231764041	231764219	E074	-14557
chr2	231764378	231764430	E074	-14346
chr2	231732667	231732755	E081	-46021
chr2	231732859	231736064	E081	-42712
chr2	231736094	231736282	E081	-42494
chr2	231736314	231736388	E081	-42388
chr2	231736559	231737141	E081	-41635
chr2	231746767	231746868	E081	-31908
chr2	231746969	231747136	E081	-31640
chr2	231747624	231747797	E081	-30979
chr2	231748346	231748465	E081	-30311
chr2	231749626	231749676	E081	-29100
chr2	231750009	231750161	E081	-28615
chr2	231750200	231750303	E081	-28473
chr2	231750597	231750805	E081	-27971
chr2	231750876	231751053	E081	-27723
chr2	231751071	231751121	E081	-27655
chr2	231751146	231751217	E081	-27559
chr2	231751503	231751574	E081	-27202
chr2	231751596	231751771	E081	-27005
chr2	231755358	231755565	E081	-23211
chr2	231755852	231755939	E081	-22837
chr2	231755982	231756084	E081	-22692
chr2	231758547	231758933	E081	-19843
chr2	231758970	231759400	E081	-19376
chr2	231764041	231764219	E081	-14557
chr2	231764378	231764430	E081	-14346
chr2	231777551	231777699	E081	-1077
chr2	231777770	231777848	E081	-928
chr2	231804847	231805072	E081	26071
chr2	231805203	231805340	E081	26427
chr2	231823297	231823360	E081	44521
chr2	231732667	231732755	E082	-46021
chr2	231746767	231746868	E082	-31908
chr2	231746969	231747136	E082	-31640
chr2	231749626	231749676	E082	-29100
chr2	231750009	231750161	E082	-28615
chr2	231750200	231750303	E082	-28473
chr2	231751503	231751574	E082	-27202
chr2	231751596	231751771	E082	-27005
chr2	231758970	231759400	E082	-19376
chr2	231764041	231764219	E082	-14557

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	231728886	231731208	E067	-47568
chr2	231821479	231822470	E067	42703
chr2	231822475	231822591	E067	43699
chr2	231728886	231731208	E068	-47568
chr2	231821479	231822470	E068	42703
chr2	231822475	231822591	E068	43699
chr2	231728886	231731208	E069	-47568
chr2	231821479	231822470	E069	42703
chr2	231822475	231822591	E069	43699
chr2	231821479	231822470	E070	42703
chr2	231822475	231822591	E070	43699
chr2	231822638	231822869	E070	43862
chr2	231728886	231731208	E071	-47568
chr2	231821479	231822470	E071	42703
chr2	231822475	231822591	E071	43699
chr2	231728886	231731208	E072	-47568
chr2	231821479	231822470	E072	42703
chr2	231822475	231822591	E072	43699
chr2	231728886	231731208	E073	-47568
chr2	231821479	231822470	E073	42703
chr2	231822475	231822591	E073	43699
chr2	231728886	231731208	E074	-47568
chr2	231821479	231822470	E074	42703
chr2	231822475	231822591	E074	43699
chr2	231728886	231731208	E081	-47568
chr2	231728886	231731208	E082	-47568
chr2	231822475	231822591	E082	43699