rs7296572

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

UTP20 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0167 (5003/29842,GnomAD)
T=0165 (4804/29118,TOPMED)
T=0206 (1030/5008,1000G)
T=0196 (754/3854,ALSPAC)
T=0199 (737/3708,TWINSUK)

Position: chr12:101296439 (GRCh38.p7) (12q23.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 9 Enhancers around

Promoter: 69 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.101296439C>T
GRCh37.p13 chr 12	NC_000012.11:g.101690217C>T

Gene: UTP20, UTP20, small subunit processome component(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UTP20 transcript	NM_014503.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.955	T=0.045
1000Genomes	American	Sub	694	C=0.750	T=0.250
1000Genomes	East Asian	Sub	1008	C=0.628	T=0.372
1000Genomes	Europe	Sub	1006	C=0.795	T=0.205
1000Genomes	Global	Study-wide	5008	C=0.794	T=0.206
1000Genomes	South Asian	Sub	978	C=0.780	T=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.804	T=0.196
The Genome Aggregation Database	African	Sub	8702	C=0.929	T=0.071
The Genome Aggregation Database	American	Sub	836	C=0.720	T=0.280
The Genome Aggregation Database	East Asian	Sub	1610	C=0.645	T=0.355
The Genome Aggregation Database	Europe	Sub	18392	C=0.809	T=0.190
The Genome Aggregation Database	Global	Study-wide	29842	C=0.832	T=0.167
The Genome Aggregation Database	Other	Sub	302	C=0.750	T=0.250
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.835	T=0.165
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.801	T=0.199

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs7296572	6.35E-06	alcohol dependence (age at onset)	24962325

eQTL of rs7296572 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 rs7296572 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 )
chr12	101691390	101691641	E067	1173
chr12	101692002	101692211	E067	1785
chr12	101692243	101692491	E067	2026
chr12	101692002	101692211	E069	1785
chr12	101692243	101692491	E069	2026
chr12	101684127	101684167	E071	-6050
chr12	101691390	101691641	E071	1173
chr12	101691390	101691641	E072	1173
chr12	101692002	101692211	E072	1785

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	101673164	101673326	E067	-16891
chr12	101673369	101673461	E067	-16756
chr12	101673570	101674315	E067	-15902
chr12	101674460	101674520	E067	-15697
chr12	101674561	101674663	E067	-15554
chr12	101692853	101693016	E067	2636
chr12	101693076	101693399	E067	2859
chr12	101693724	101694082	E067	3507
chr12	101673164	101673326	E068	-16891
chr12	101673369	101673461	E068	-16756
chr12	101673570	101674315	E068	-15902
chr12	101674460	101674520	E068	-15697
chr12	101674561	101674663	E068	-15554
chr12	101692853	101693016	E068	2636
chr12	101693076	101693399	E068	2859
chr12	101673164	101673326	E069	-16891
chr12	101673369	101673461	E069	-16756
chr12	101673570	101674315	E069	-15902
chr12	101674460	101674520	E069	-15697
chr12	101674561	101674663	E069	-15554
chr12	101692853	101693016	E069	2636
chr12	101693076	101693399	E069	2859
chr12	101693724	101694082	E069	3507
chr12	101673164	101673326	E070	-16891
chr12	101673369	101673461	E070	-16756
chr12	101673570	101674315	E070	-15902
chr12	101674460	101674520	E070	-15697
chr12	101674561	101674663	E070	-15554
chr12	101673056	101673115	E071	-17102
chr12	101673121	101673150	E071	-17067
chr12	101673164	101673326	E071	-16891
chr12	101673369	101673461	E071	-16756
chr12	101673570	101674315	E071	-15902
chr12	101674460	101674520	E071	-15697
chr12	101674561	101674663	E071	-15554
chr12	101692853	101693016	E071	2636
chr12	101693076	101693399	E071	2859
chr12	101693724	101694082	E071	3507
chr12	101673164	101673326	E072	-16891
chr12	101673369	101673461	E072	-16756
chr12	101673570	101674315	E072	-15902
chr12	101674460	101674520	E072	-15697
chr12	101674561	101674663	E072	-15554
chr12	101692853	101693016	E072	2636
chr12	101693076	101693399	E072	2859
chr12	101673164	101673326	E073	-16891
chr12	101673369	101673461	E073	-16756
chr12	101673570	101674315	E073	-15902
chr12	101674460	101674520	E073	-15697
chr12	101674561	101674663	E073	-15554
chr12	101673164	101673326	E074	-16891
chr12	101673369	101673461	E074	-16756
chr12	101673570	101674315	E074	-15902
chr12	101674460	101674520	E074	-15697
chr12	101674561	101674663	E074	-15554
chr12	101692853	101693016	E074	2636
chr12	101693076	101693399	E074	2859
chr12	101693724	101694082	E074	3507
chr12	101673369	101673461	E081	-16756
chr12	101673570	101674315	E081	-15902
chr12	101674460	101674520	E081	-15697
chr12	101674561	101674663	E081	-15554
chr12	101673056	101673115	E082	-17102
chr12	101673121	101673150	E082	-17067
chr12	101673164	101673326	E082	-16891
chr12	101673369	101673461	E082	-16756
chr12	101673570	101674315	E082	-15902
chr12	101674460	101674520	E082	-15697
chr12	101674561	101674663	E082	-15554