rs1472556

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

UTP20 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0171 (5127/29910,GnomAD)
A=0168 (4903/29118,TOPMED)
A=0211 (1055/5008,1000G)
A=0199 (768/3854,ALSPAC)
A=0201 (745/3708,TWINSUK)

Position: chr12:101311400 (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.101311400C>A
GRCh37.p13 chr 12	NC_000012.11:g.101705178C>A

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	A=0.045
1000Genomes	American	Sub	694	C=0.720	A=0.280
1000Genomes	East Asian	Sub	1008	C=0.625	A=0.375
1000Genomes	Europe	Sub	1006	C=0.793	A=0.207
1000Genomes	Global	Study-wide	5008	C=0.789	A=0.211
1000Genomes	South Asian	Sub	978	C=0.780	A=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.801	A=0.199
The Genome Aggregation Database	African	Sub	8718	C=0.928	A=0.072
The Genome Aggregation Database	American	Sub	834	C=0.690	A=0.310
The Genome Aggregation Database	East Asian	Sub	1610	C=0.648	A=0.352
The Genome Aggregation Database	Europe	Sub	18446	C=0.804	A=0.195
The Genome Aggregation Database	Global	Study-wide	29910	C=0.828	A=0.171
The Genome Aggregation Database	Other	Sub	302	C=0.750	A=0.250
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.831	A=0.168
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.799	A=0.201

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
rs1472556	6.35E-06	alcohol dependence (age at onset)	24962325

eQTL of rs1472556 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 rs1472556 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	-13537
chr12	101692002	101692211	E067	-12967
chr12	101692243	101692491	E067	-12687
chr12	101692002	101692211	E069	-12967
chr12	101692243	101692491	E069	-12687
chr12	101684127	101684167	E071	-21011
chr12	101691390	101691641	E071	-13537
chr12	101691390	101691641	E072	-13537
chr12	101692002	101692211	E072	-12967

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	101673164	101673326	E067	-31852
chr12	101673369	101673461	E067	-31717
chr12	101673570	101674315	E067	-30863
chr12	101674460	101674520	E067	-30658
chr12	101674561	101674663	E067	-30515
chr12	101692853	101693016	E067	-12162
chr12	101693076	101693399	E067	-11779
chr12	101693724	101694082	E067	-11096
chr12	101673164	101673326	E068	-31852
chr12	101673369	101673461	E068	-31717
chr12	101673570	101674315	E068	-30863
chr12	101674460	101674520	E068	-30658
chr12	101674561	101674663	E068	-30515
chr12	101692853	101693016	E068	-12162
chr12	101693076	101693399	E068	-11779
chr12	101673164	101673326	E069	-31852
chr12	101673369	101673461	E069	-31717
chr12	101673570	101674315	E069	-30863
chr12	101674460	101674520	E069	-30658
chr12	101674561	101674663	E069	-30515
chr12	101692853	101693016	E069	-12162
chr12	101693076	101693399	E069	-11779
chr12	101693724	101694082	E069	-11096
chr12	101673164	101673326	E070	-31852
chr12	101673369	101673461	E070	-31717
chr12	101673570	101674315	E070	-30863
chr12	101674460	101674520	E070	-30658
chr12	101674561	101674663	E070	-30515
chr12	101673056	101673115	E071	-32063
chr12	101673121	101673150	E071	-32028
chr12	101673164	101673326	E071	-31852
chr12	101673369	101673461	E071	-31717
chr12	101673570	101674315	E071	-30863
chr12	101674460	101674520	E071	-30658
chr12	101674561	101674663	E071	-30515
chr12	101692853	101693016	E071	-12162
chr12	101693076	101693399	E071	-11779
chr12	101693724	101694082	E071	-11096
chr12	101673164	101673326	E072	-31852
chr12	101673369	101673461	E072	-31717
chr12	101673570	101674315	E072	-30863
chr12	101674460	101674520	E072	-30658
chr12	101674561	101674663	E072	-30515
chr12	101692853	101693016	E072	-12162
chr12	101693076	101693399	E072	-11779
chr12	101673164	101673326	E073	-31852
chr12	101673369	101673461	E073	-31717
chr12	101673570	101674315	E073	-30863
chr12	101674460	101674520	E073	-30658
chr12	101674561	101674663	E073	-30515
chr12	101673164	101673326	E074	-31852
chr12	101673369	101673461	E074	-31717
chr12	101673570	101674315	E074	-30863
chr12	101674460	101674520	E074	-30658
chr12	101674561	101674663	E074	-30515
chr12	101692853	101693016	E074	-12162
chr12	101693076	101693399	E074	-11779
chr12	101693724	101694082	E074	-11096
chr12	101673369	101673461	E081	-31717
chr12	101673570	101674315	E081	-30863
chr12	101674460	101674520	E081	-30658
chr12	101674561	101674663	E081	-30515
chr12	101673056	101673115	E082	-32063
chr12	101673121	101673150	E082	-32028
chr12	101673164	101673326	E082	-31852
chr12	101673369	101673461	E082	-31717
chr12	101673570	101674315	E082	-30863
chr12	101674460	101674520	E082	-30658
chr12	101674561	101674663	E082	-30515