rs10939516

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LINC01182 : Intron Variant
LOC101929048 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0170 (5105/29922,GnomAD)
G=0161 (4698/29118,TOPMED)
G=0126 (630/5008,1000G)
G=0187 (722/3854,ALSPAC)
G=0181 (671/3708,TWINSUK)

Position: chr4:13813531 (GRCh38.p7) (4p15.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 63 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.13813531A>G
GRCh37.p13 chr 4	NC_000004.11:g.13815155A>G

Gene: LINC01182, long intergenic non-protein coding RNA 1182(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01182 transcript	NR_121681.1:n.	N/A	Intron Variant

Gene: LOC101929048, uncharacterized LOC101929048(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101929048 transcript variant X1	XR_001741385.1:n.	N/A	Intron Variant
LOC101929048 transcript variant X2	XR_001741386.1:n.	N/A	Intron Variant
LOC101929048 transcript variant X5	XR_001741387.1:n.	N/A	Intron Variant
LOC101929048 transcript variant X3	XR_925415.2:n.	N/A	Intron Variant
LOC101929048 transcript variant X6	XR_925417.2:n.	N/A	Intron Variant
LOC101929048 transcript variant X4	XR_925418.2:n.	N/A	Intron Variant
LOC101929048 transcript variant X7	XR_925419.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.906	G=0.094
1000Genomes	American	Sub	694	A=0.830	G=0.170
1000Genomes	East Asian	Sub	1008	A=0.878	G=0.122
1000Genomes	Europe	Sub	1006	A=0.826	G=0.174
1000Genomes	Global	Study-wide	5008	A=0.874	G=0.126
1000Genomes	South Asian	Sub	978	A=0.910	G=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.813	G=0.187
The Genome Aggregation Database	African	Sub	8718	A=0.888	G=0.112
The Genome Aggregation Database	American	Sub	838	A=0.800	G=0.200
The Genome Aggregation Database	East Asian	Sub	1612	A=0.885	G=0.115
The Genome Aggregation Database	Europe	Sub	18452	A=0.798	G=0.201
The Genome Aggregation Database	Global	Study-wide	29922	A=0.829	G=0.170
The Genome Aggregation Database	Other	Sub	302	A=0.840	G=0.160
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.838	G=0.161
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.819	G=0.181

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
rs10939516	0.000511	alcohol dependence	20201924

eQTL of rs10939516 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 rs10939516 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	13768445	13768690	E067	-46465
chr4	13783811	13783868	E067	-31287
chr4	13783916	13783966	E067	-31189
chr4	13783968	13784039	E067	-31116
chr4	13785355	13785751	E067	-29404
chr4	13785760	13786018	E067	-29137
chr4	13786157	13786207	E067	-28948
chr4	13846063	13846112	E067	30908
chr4	13846536	13846598	E067	31381
chr4	13852045	13852089	E067	36890
chr4	13852157	13852438	E067	37002
chr4	13853019	13853139	E067	37864
chr4	13853801	13854005	E067	38646
chr4	13785355	13785751	E068	-29404
chr4	13786157	13786207	E068	-28948
chr4	13852045	13852089	E068	36890
chr4	13852157	13852438	E068	37002
chr4	13853019	13853139	E068	37864
chr4	13853801	13854005	E068	38646
chr4	13785355	13785751	E069	-29404
chr4	13846536	13846598	E069	31381
chr4	13852045	13852089	E069	36890
chr4	13852157	13852438	E069	37002
chr4	13853019	13853139	E069	37864
chr4	13853801	13854005	E069	38646
chr4	13832219	13832299	E070	17064
chr4	13853019	13853139	E070	37864
chr4	13853801	13854005	E070	38646
chr4	13785760	13786018	E071	-29137
chr4	13786037	13786140	E071	-29015
chr4	13786157	13786207	E071	-28948
chr4	13851578	13851669	E071	36423
chr4	13852045	13852089	E071	36890
chr4	13852157	13852438	E071	37002
chr4	13853019	13853139	E071	37864
chr4	13853801	13854005	E071	38646
chr4	13785760	13786018	E072	-29137
chr4	13786037	13786140	E072	-29015
chr4	13786157	13786207	E072	-28948
chr4	13789540	13789638	E072	-25517
chr4	13852157	13852438	E072	37002
chr4	13853019	13853139	E072	37864
chr4	13853801	13854005	E072	38646
chr4	13785355	13785751	E073	-29404
chr4	13852045	13852089	E073	36890
chr4	13852157	13852438	E073	37002
chr4	13853019	13853139	E073	37864
chr4	13768445	13768690	E074	-46465
chr4	13783811	13783868	E074	-31287
chr4	13783916	13783966	E074	-31189
chr4	13783968	13784039	E074	-31116
chr4	13784046	13784128	E074	-31027
chr4	13784195	13784314	E074	-30841
chr4	13785355	13785751	E074	-29404
chr4	13785760	13786018	E074	-29137
chr4	13786037	13786140	E074	-29015
chr4	13786157	13786207	E074	-28948
chr4	13831791	13831959	E074	16636
chr4	13852045	13852089	E074	36890
chr4	13852157	13852438	E074	37002
chr4	13853019	13853139	E074	37864
chr4	13853801	13854005	E074	38646
chr4	13832219	13832299	E081	17064