rs16979890

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

OPA3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0141 (4225/29970,GnomAD)
A=0120 (3516/29118,TOPMED)
A=0151 (754/5008,1000G)
A=0157 (607/3854,ALSPAC)
A=0160 (592/3708,TWINSUK)

Position: chr19:45563060 (GRCh38.p7) (19q13.32)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 41 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.45563060G>A
GRCh37.p13 chr 19	NC_000019.9:g.46066318G>A
OPA3 RefSeqGene	NG_013332.1:g.26805C>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=0.961	A=0.039
1000Genomes	American	Sub	694	G=0.820	A=0.180
1000Genomes	East Asian	Sub	1008	G=0.747	A=0.253
1000Genomes	Europe	Sub	1006	G=0.858	A=0.142
1000Genomes	Global	Study-wide	5008	G=0.849	A=0.151
1000Genomes	South Asian	Sub	978	G=0.820	A=0.180
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.843	A=0.157
The Genome Aggregation Database	African	Sub	8728	G=0.941	A=0.059
The Genome Aggregation Database	American	Sub	838	G=0.800	A=0.200
The Genome Aggregation Database	East Asian	Sub	1616	G=0.762	A=0.238
The Genome Aggregation Database	Europe	Sub	18486	G=0.833	A=0.167
The Genome Aggregation Database	Global	Study-wide	29970	G=0.859	A=0.141
The Genome Aggregation Database	Other	Sub	302	G=0.780	A=0.220
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.879	A=0.120
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.840	A=0.160

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
rs16979890	0.00034	alcohol dependence	20201924

eQTL of rs16979890 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 rs16979890 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	-18713
chr19	46057718	46057772	E067	-8546
chr19	46029169	46029293	E068	-37025
chr19	46029305	46029777	E068	-36541
chr19	46033068	46033296	E068	-33022
chr19	46047088	46047605	E068	-18713
chr19	46098710	46098802	E068	32392
chr19	46100209	46100298	E068	33891
chr19	46100621	46100722	E068	34303
chr19	46029169	46029293	E069	-37025
chr19	46029305	46029777	E069	-36541
chr19	46047088	46047605	E069	-18713
chr19	46016774	46016830	E071	-49488
chr19	46017102	46017222	E071	-49096
chr19	46017253	46017651	E071	-48667
chr19	46017695	46019000	E071	-47318
chr19	46019009	46019743	E071	-46575
chr19	46047088	46047605	E071	-18713
chr19	46051287	46051857	E071	-14461
chr19	46061589	46062154	E071	-4164
chr19	46115988	46116028	E071	49670
chr19	46116085	46116135	E071	49767
chr19	46027577	46027712	E072	-38606
chr19	46027753	46027826	E072	-38492
chr19	46027846	46027956	E072	-38362
chr19	46047088	46047605	E072	-18713
chr19	46056614	46056683	E072	-9635
chr19	46084935	46085121	E072	18617
chr19	46016513	46016722	E073	-49596
chr19	46016774	46016830	E073	-49488
chr19	46017102	46017222	E073	-49096
chr19	46017253	46017651	E073	-48667
chr19	46051287	46051857	E073	-14461
chr19	46073055	46073687	E073	6737
chr19	46029169	46029293	E074	-37025
chr19	46029305	46029777	E074	-36541
chr19	46047088	46047605	E074	-18713
chr19	46084464	46084898	E074	18146
chr19	46084935	46085121	E074	18617
chr19	46098710	46098802	E074	32392
chr19	46033068	46033296	E081	-33022

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	46057148	46057205	E067	-9113
chr19	46087030	46089123	E067	20712
chr19	46104688	46104837	E067	38370
chr19	46104854	46104927	E067	38536
chr19	46105012	46105062	E067	38694
chr19	46105099	46105912	E067	38781
chr19	46087030	46089123	E068	20712
chr19	46104417	46104668	E068	38099
chr19	46104688	46104837	E068	38370
chr19	46104854	46104927	E068	38536
chr19	46105012	46105062	E068	38694
chr19	46105099	46105912	E068	38781
chr19	46087030	46089123	E069	20712
chr19	46104417	46104668	E069	38099
chr19	46104688	46104837	E069	38370
chr19	46104854	46104927	E069	38536
chr19	46105012	46105062	E069	38694
chr19	46087030	46089123	E070	20712
chr19	46087030	46089123	E071	20712
chr19	46104417	46104668	E071	38099
chr19	46104688	46104837	E071	38370
chr19	46104854	46104927	E071	38536
chr19	46105012	46105062	E071	38694
chr19	46105099	46105912	E071	38781
chr19	46056752	46057105	E072	-9213
chr19	46057148	46057205	E072	-9113
chr19	46087030	46089123	E072	20712
chr19	46104417	46104668	E072	38099
chr19	46104688	46104837	E072	38370
chr19	46104854	46104927	E072	38536
chr19	46105012	46105062	E072	38694
chr19	46056752	46057105	E073	-9213
chr19	46057148	46057205	E073	-9113
chr19	46087030	46089123	E073	20712
chr19	46104417	46104668	E073	38099
chr19	46104688	46104837	E073	38370
chr19	46104854	46104927	E073	38536
chr19	46105012	46105062	E073	38694
chr19	46105099	46105912	E073	38781
chr19	46087030	46089123	E074	20712
chr19	46104417	46104668	E074	38099
chr19	46104688	46104837	E074	38370
chr19	46104854	46104927	E074	38536
chr19	46105012	46105062	E074	38694
chr19	46105099	46105912	E074	38781
chr19	46087030	46089123	E081	20712
chr19	46056752	46057105	E082	-9213
chr19	46057148	46057205	E082	-9113
chr19	46087030	46089123	E082	20712
chr19	46104688	46104837	E082	38370
chr19	46104854	46104927	E082	38536
chr19	46105012	46105062	E082	38694