rs1264226

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

OPA3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0400 (11969/29866,GnomAD)
G==0417 (12164/29118,TOPMED)
G==0383 (1918/5008,1000G)
G==0407 (1570/3854,ALSPAC)
G==0407 (1508/3708,TWINSUK)

Position: chr19:45559909 (GRCh38.p7) (19q13.32)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 39 Enhancers around

Promoter: 52 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.45559909G>A
GRCh37.p13 chr 19	NC_000019.9:g.46063167G>A
OPA3 RefSeqGene	NG_013332.1:g.29956C>T

Gene: OPA3, optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OPA3 transcript variant 1	NM_001017989.2:c.	N/A	Intron Variant
OPA3 transcript variant 2	NM_025136.3:c.	N/A	Intron Variant
OPA3 transcript variant X1	XM_006723403.3:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.439	A=0.561
1000Genomes	American	Sub	694	G=0.330	A=0.670
1000Genomes	East Asian	Sub	1008	G=0.269	A=0.731
1000Genomes	Europe	Sub	1006	G=0.403	A=0.597
1000Genomes	Global	Study-wide	5008	G=0.383	A=0.617
1000Genomes	South Asian	Sub	978	G=0.440	A=0.560
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.407	A=0.593
The Genome Aggregation Database	African	Sub	8684	G=0.433	A=0.567
The Genome Aggregation Database	American	Sub	836	G=0.370	A=0.630
The Genome Aggregation Database	East Asian	Sub	1606	G=0.287	A=0.713
The Genome Aggregation Database	Europe	Sub	18438	G=0.395	A=0.604
The Genome Aggregation Database	Global	Study-wide	29866	G=0.400	A=0.599
The Genome Aggregation Database	Other	Sub	302	G=0.480	A=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.417	A=0.582
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.407	A=0.593

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
rs1264226	0.00068	alcohol dependence	20201924

eQTL of rs1264226 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:46063167	OPA3	ENSG00000125741.4	G>A	1.4069e-10	-42303	Cerebellum
Chr19:46063167	OPA3	ENSG00000125741.4	G>A	7.7980e-9	-42303	Cerebellar_Hemisphere

meQTL of rs1264226 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 )
chr19	46047088	46047605	E067	-15562
chr19	46057718	46057772	E067	-5395
chr19	46029169	46029293	E068	-33874
chr19	46029305	46029777	E068	-33390
chr19	46033068	46033296	E068	-29871
chr19	46047088	46047605	E068	-15562
chr19	46098710	46098802	E068	35543
chr19	46100209	46100298	E068	37042
chr19	46100621	46100722	E068	37454
chr19	46029169	46029293	E069	-33874
chr19	46029305	46029777	E069	-33390
chr19	46047088	46047605	E069	-15562
chr19	46016774	46016830	E071	-46337
chr19	46017102	46017222	E071	-45945
chr19	46017253	46017651	E071	-45516
chr19	46017695	46019000	E071	-44167
chr19	46019009	46019743	E071	-43424
chr19	46047088	46047605	E071	-15562
chr19	46051287	46051857	E071	-11310
chr19	46061589	46062154	E071	-1013
chr19	46027577	46027712	E072	-35455
chr19	46027753	46027826	E072	-35341
chr19	46027846	46027956	E072	-35211
chr19	46047088	46047605	E072	-15562
chr19	46056614	46056683	E072	-6484
chr19	46084935	46085121	E072	21768
chr19	46016513	46016722	E073	-46445
chr19	46016774	46016830	E073	-46337
chr19	46017102	46017222	E073	-45945
chr19	46017253	46017651	E073	-45516
chr19	46051287	46051857	E073	-11310
chr19	46073055	46073687	E073	9888
chr19	46029169	46029293	E074	-33874
chr19	46029305	46029777	E074	-33390
chr19	46047088	46047605	E074	-15562
chr19	46084464	46084898	E074	21297
chr19	46084935	46085121	E074	21768
chr19	46098710	46098802	E074	35543
chr19	46033068	46033296	E081	-29871

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	46057148	46057205	E067	-5962
chr19	46087030	46089123	E067	23863
chr19	46104688	46104837	E067	41521
chr19	46104854	46104927	E067	41687
chr19	46105012	46105062	E067	41845
chr19	46105099	46105912	E067	41932
chr19	46087030	46089123	E068	23863
chr19	46104417	46104668	E068	41250
chr19	46104688	46104837	E068	41521
chr19	46104854	46104927	E068	41687
chr19	46105012	46105062	E068	41845
chr19	46105099	46105912	E068	41932
chr19	46087030	46089123	E069	23863
chr19	46104417	46104668	E069	41250
chr19	46104688	46104837	E069	41521
chr19	46104854	46104927	E069	41687
chr19	46105012	46105062	E069	41845
chr19	46087030	46089123	E070	23863
chr19	46087030	46089123	E071	23863
chr19	46104417	46104668	E071	41250
chr19	46104688	46104837	E071	41521
chr19	46104854	46104927	E071	41687
chr19	46105012	46105062	E071	41845
chr19	46105099	46105912	E071	41932
chr19	46056752	46057105	E072	-6062
chr19	46057148	46057205	E072	-5962
chr19	46087030	46089123	E072	23863
chr19	46104417	46104668	E072	41250
chr19	46104688	46104837	E072	41521
chr19	46104854	46104927	E072	41687
chr19	46105012	46105062	E072	41845
chr19	46056752	46057105	E073	-6062
chr19	46057148	46057205	E073	-5962
chr19	46087030	46089123	E073	23863
chr19	46104417	46104668	E073	41250
chr19	46104688	46104837	E073	41521
chr19	46104854	46104927	E073	41687
chr19	46105012	46105062	E073	41845
chr19	46105099	46105912	E073	41932
chr19	46087030	46089123	E074	23863
chr19	46104417	46104668	E074	41250
chr19	46104688	46104837	E074	41521
chr19	46104854	46104927	E074	41687
chr19	46105012	46105062	E074	41845
chr19	46105099	46105912	E074	41932
chr19	46087030	46089123	E081	23863
chr19	46056752	46057105	E082	-6062
chr19	46057148	46057205	E082	-5962
chr19	46087030	46089123	E082	23863
chr19	46104688	46104837	E082	41521
chr19	46104854	46104927	E082	41687
chr19	46105012	46105062	E082	41845