rs6716455

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105373684 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0111 (3354/29966,GnomAD)
A=0094 (2741/29118,TOPMED)
A=0117 (584/5008,1000G)
A=0130 (500/3854,ALSPAC)
A=0133 (495/3708,TWINSUK)

Position: chr2:150269889 (GRCh38.p7) (2q23.3)

Phenotype: AD

Dataset:

GWASdb2 | GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 57 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.150269889G>A
GRCh37.p13 chr 2	NC_000002.11:g.151126403G>A

Gene: LOC105373684, uncharacterized LOC105373684(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01818 transcript variant X1	XR_923469.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.983	A=0.017
1000Genomes	American	Sub	694	G=0.860	A=0.140
1000Genomes	East Asian	Sub	1008	G=0.823	A=0.177
1000Genomes	Europe	Sub	1006	G=0.843	A=0.157
1000Genomes	Global	Study-wide	5008	G=0.883	A=0.117
1000Genomes	South Asian	Sub	978	G=0.870	A=0.130
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.870	A=0.130
The Genome Aggregation Database	African	Sub	8732	G=0.961	A=0.039
The Genome Aggregation Database	American	Sub	836	G=0.890	A=0.110
The Genome Aggregation Database	East Asian	Sub	1614	G=0.794	A=0.206
The Genome Aggregation Database	Europe	Sub	18482	G=0.863	A=0.136
The Genome Aggregation Database	Global	Study-wide	29966	G=0.888	A=0.111
The Genome Aggregation Database	Other	Sub	302	G=0.820	A=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.905	A=0.094
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.867	A=0.133

PMID	Title	Author	Journal
21529783	A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.	Heath AC	Biol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs6716455	0.0000007	alcoholism (alcohol use disorder factor score)	21529783
rs6716455	0.000009	alcohol dependence	21529783
rs6716455

eQTL of rs6716455 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 rs6716455 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	151091207	151091247	E068	-35156
chr2	151091285	151092080	E068	-34323
chr2	151153160	151153870	E068	26757
chr2	151153925	151153975	E068	27522
chr2	151091207	151091247	E069	-35156
chr2	151091285	151092080	E069	-34323
chr2	151151864	151152268	E069	25461
chr2	151078948	151079224	E070	-47179
chr2	151079408	151079495	E070	-46908
chr2	151079543	151079691	E070	-46712
chr2	151085053	151085103	E070	-41300
chr2	151085518	151085788	E070	-40615
chr2	151086291	151086407	E070	-39996
chr2	151088085	151088297	E070	-38106
chr2	151088846	151089767	E070	-36636
chr2	151112209	151112376	E070	-14027
chr2	151112638	151112741	E070	-13662
chr2	151112754	151112854	E070	-13549
chr2	151113181	151113283	E070	-13120
chr2	151113285	151113342	E070	-13061
chr2	151113424	151113513	E070	-12890
chr2	151114864	151114957	E070	-11446
chr2	151116274	151116727	E070	-9676
chr2	151117340	151117626	E070	-8777
chr2	151140800	151140871	E070	14397
chr2	151143082	151143207	E070	16679
chr2	151143355	151143958	E070	16952
chr2	151152600	151152790	E070	26197
chr2	151152801	151153003	E070	26398
chr2	151153160	151153870	E070	26757
chr2	151153925	151153975	E070	27522
chr2	151091207	151091247	E071	-35156
chr2	151091285	151092080	E071	-34323
chr2	151153160	151153870	E071	26757
chr2	151153925	151153975	E071	27522
chr2	151091207	151091247	E072	-35156
chr2	151091285	151092080	E072	-34323
chr2	151153160	151153870	E072	26757
chr2	151153925	151153975	E072	27522
chr2	151153160	151153870	E074	26757
chr2	151153925	151153975	E074	27522
chr2	151091207	151091247	E081	-35156
chr2	151091285	151092080	E081	-34323
chr2	151114864	151114957	E081	-11446
chr2	151116274	151116727	E081	-9676
chr2	151153160	151153870	E081	26757
chr2	151153925	151153975	E081	27522
chr2	151155261	151155358	E081	28858
chr2	151155536	151155704	E081	29133
chr2	151078948	151079224	E082	-47179
chr2	151079408	151079495	E082	-46908
chr2	151079543	151079691	E082	-46712
chr2	151082329	151082633	E082	-43770
chr2	151091285	151092080	E082	-34323
chr2	151143355	151143958	E082	16952
chr2	151153160	151153870	E082	26757
chr2	151153925	151153975	E082	27522