SNP Detail Info-rs752522

Organism: Homo sapiens

Alleles: C>G / C>T

Gene : Feature

MED25 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0107 (3208/29856,GnomAD)
T=0112 (3272/29118,TOPMED)
C==0119 (1559/13006,GO-ESP)
T=0090 (449/5008,1000G)
T=0155 (599/3854,ALSPAC)
T=0149 (551/3708,TWINSUK)

Position: chr19:49835196 (GRCh38.p7) (19q13.33)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 15 Enhancers around

Promoter: 18 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.49835196C>G
GRCh38.p7 chr 19	NC_000019.10:g.49835196C>T
GRCh37.p13 chr 19	NC_000019.9:g.50338453C>G
GRCh37.p13 chr 19	NC_000019.9:g.50338453C>T
MED25 RefSeqGene	LRG_368
MED25 RefSeqGene	LRG_368

Gene: MED25, mediator complex subunit 25(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MED25 transcript	NM_030973.3:c.	N/A	Intron Variant
MED25 transcript variant X1	XM_011527353.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.961	T=0.039
1000Genomes	American	Sub	694	C=0.920	T=0.080
1000Genomes	East Asian	Sub	1008	C=0.863	T=0.137
1000Genomes	Europe	Sub	1006	C=0.875	T=0.125
1000Genomes	Global	Study-wide	5008	C=0.910	T=0.090
1000Genomes	South Asian	Sub	978	C=0.920	T=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.845	T=0.155
The Genome Aggregation Database	African	Sub	8686	C=0.933	T=0.067
The Genome Aggregation Database	American	Sub	838	C=0.920	T=0.08,
The Genome Aggregation Database	East Asian	Sub	1614	C=0.839	T=0.161
The Genome Aggregation Database	Europe	Sub	18418	C=0.877	T=0.122
The Genome Aggregation Database	Global	Study-wide	29856	C=0.892	T=0.107
The Genome Aggregation Database	Other	Sub	300	C=0.850	T=0.15,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.887	T=0.112
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.851	T=0.149

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs752522	7.84E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs752522 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 rs752522 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr19	24257938	24258002	E067	-35300
chr19	24271275	24271325	E067	-21977
chr19	24284172	24284297	E067	-9005
chr19	24284400	24284804	E067	-8498
chr19	24284172	24284297	E068	-9005
chr19	24284400	24284804	E068	-8498
chr19	24271275	24271325	E069	-21977
chr19	24284400	24284804	E069	-8498
chr19	24284400	24284804	E071	-8498
chr19	24282435	24282546	E074	-10756
chr19	24282650	24282882	E074	-10420
chr19	24284172	24284297	E074	-9005
chr19	24284400	24284804	E074	-8498
chr19	24271275	24271325	E081	-21977
chr19	24271461	24271575	E081	-21727

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	24269332	24270714	E067	-22588
chr19	24269332	24270714	E068	-22588
chr19	24271015	24271080	E068	-22222
chr19	24271151	24271252	E068	-22050
chr19	24269332	24270714	E069	-22588
chr19	24271015	24271080	E069	-22222
chr19	24271151	24271252	E069	-22050
chr19	24269332	24270714	E070	-22588
chr19	24271015	24271080	E070	-22222
chr19	24269332	24270714	E071	-22588
chr19	24269332	24270714	E072	-22588
chr19	24269332	24270714	E073	-22588
chr19	24271015	24271080	E073	-22222
chr19	24269332	24270714	E074	-22588
chr19	24269332	24270714	E081	-22588
chr19	24269332	24270714	E082	-22588
chr19	24271015	24271080	E082	-22222
chr19	24271151	24271252	E082	-22050

rs752522