SNP Detail Info-rs2270861

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

UTP20 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0253 (29767/117604,ExAC)
G=0222 (6647/29932,GnomAD)
G=0226 (6591/29118,TOPMED)
A==0218 (2844/13002,GO-ESP)
G=0257 (1285/5008,1000G)
G=0230 (886/3854,ALSPAC)
G=0233 (865/3708,TWINSUK)

Position: chr12:101342603 (GRCh38.p7) (12q23.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 16 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.101342603A>G
GRCh37.p13 chr 12	NC_000012.11:g.101736381A>G

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	A=0.846	G=0.154
1000Genomes	American	Sub	694	A=0.680	G=0.320
1000Genomes	East Asian	Sub	1008	A=0.624	G=0.376
1000Genomes	Europe	Sub	1006	A=0.762	G=0.238
1000Genomes	Global	Study-wide	5008	A=0.743	G=0.257
1000Genomes	South Asian	Sub	978	A=0.750	G=0.250
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.770	G=0.230
The Exome Aggregation Consortium	American	Sub	21446	A=0.727	G=0.272
The Exome Aggregation Consortium	Asian	Sub	23970	A=0.701	G=0.299
The Exome Aggregation Consortium	Europe	Sub	71306	A=0.768	G=0.231
The Exome Aggregation Consortium	Global	Study-wide	117604	A=0.746	G=0.253
The Exome Aggregation Consortium	Other	Sub	882	A=0.730	G=0.270
The Genome Aggregation Database	African	Sub	8720	A=0.828	G=0.172
The Genome Aggregation Database	American	Sub	836	A=0.660	G=0.340
The Genome Aggregation Database	East Asian	Sub	1616	A=0.643	G=0.357
The Genome Aggregation Database	Europe	Sub	18460	A=0.772	G=0.227
The Genome Aggregation Database	Global	Study-wide	29932	A=0.777	G=0.222
The Genome Aggregation Database	Other	Sub	300	A=0.710	G=0.290
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.773	G=0.226
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.767	G=0.233

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
17903303	Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study.	O'Donnell CJ	BMC Med Genet

P-Value

SNP ID	p-value	Traits	Study
rs2270861	6.79E-08	alcohol dependence (age at onset)	24962325

eQTL of rs2270861 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 rs2270861 in Fetal Brain

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr12	101691390	101691641	E067	-44740
chr12	101692002	101692211	E067	-44170
chr12	101692243	101692491	E067	-43890
chr12	101692002	101692211	E069	-44170
chr12	101692243	101692491	E069	-43890
chr12	101691390	101691641	E071	-44740
chr12	101691390	101691641	E072	-44740
chr12	101692002	101692211	E072	-44170

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	101692853	101693016	E067	-43365
chr12	101693076	101693399	E067	-42982
chr12	101693724	101694082	E067	-42299
chr12	101692853	101693016	E068	-43365
chr12	101693076	101693399	E068	-42982
chr12	101692853	101693016	E069	-43365
chr12	101693076	101693399	E069	-42982
chr12	101693724	101694082	E069	-42299
chr12	101692853	101693016	E071	-43365
chr12	101693076	101693399	E071	-42982
chr12	101693724	101694082	E071	-42299
chr12	101692853	101693016	E072	-43365
chr12	101693076	101693399	E072	-42982
chr12	101692853	101693016	E074	-43365
chr12	101693076	101693399	E074	-42982
chr12	101693724	101694082	E074	-42299

rs2270861