rs4663276

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0127 (3728/29266,GnomAD)
G==0134 (3912/29118,TOPMED)
G==0152 (760/5008,1000G)
G==0177 (682/3854,ALSPAC)
G==0190 (705/3708,TWINSUK)

Position: chr2:237990167 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 115 Enhancers around

Promoter: 32 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.237990167G>A
GRCh37.p13 chr 2	NC_000002.11:g.238898809G>A

Gene: UBE2F, ubiquitin conjugating enzyme E2 F (putative)(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBE2F transcript variant 2	NM_001278305.1:c.	N/A	Intron Variant
UBE2F transcript variant 3	NM_001278306.1:c.	N/A	Intron Variant
UBE2F transcript variant 4	NM_001278307.1:c.	N/A	Intron Variant
UBE2F transcript variant 5	NM_001278308.1:c.	N/A	Intron Variant
UBE2F transcript variant 1	NM_080678.2:c.	N/A	Intron Variant
UBE2F transcript variant 6	NR_103498.1:n.	N/A	Intron Variant
UBE2F transcript variant 7	NR_103499.1:n.	N/A	Intron Variant
UBE2F transcript variant 8	NR_103500.1:n.	N/A	Intron Variant

Gene: UBE2F-SCLY, UBE2F-SCLY readthrough (NMD candidate)(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBE2F-SCLY transcript	NR_037904.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.099	A=0.901
1000Genomes	American	Sub	694	G=0.180	A=0.820
1000Genomes	East Asian	Sub	1008	G=0.030	A=0.970
1000Genomes	Europe	Sub	1006	G=0.164	A=0.836
1000Genomes	Global	Study-wide	5008	G=0.152	A=0.848
1000Genomes	South Asian	Sub	978	G=0.310	A=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.177	A=0.823
The Genome Aggregation Database	African	Sub	8570	G=0.109	A=0.891
The Genome Aggregation Database	American	Sub	804	G=0.170	A=0.830
The Genome Aggregation Database	East Asian	Sub	1606	G=0.029	A=0.971
The Genome Aggregation Database	Europe	Sub	17986	G=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29266	G=0.127	A=0.872
The Genome Aggregation Database	Other	Sub	300	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.134	A=0.865
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.190	A=0.810

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs4663276	0.000146	alcohol consumption	23743675

eQTL of rs4663276 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238898809	SCLY	ENSG00000132330.12	G>A	7.8532e-10	-70721	Cerebellum
Chr2:238898809	SCLY	ENSG00000132330.12	G>A	1.0714e-8	-70721	Cortex
Chr2:238898809	SCLY	ENSG00000132330.12	G>A	2.0850e-8	-70721	Cerebellar_Hemisphere
Chr2:238898809	SCLY	ENSG00000132330.12	G>A	2.3006e-3	-70721	Substantia_nigra

meQTL of rs4663276 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0646226347905888	2.4442e-14

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 )
chr2	238877816	238878038	E067	-20771
chr2	238878398	238878539	E067	-20270
chr2	238878551	238878601	E067	-20208
chr2	238878666	238878738	E067	-20071
chr2	238879158	238879263	E067	-19546
chr2	238886584	238886634	E067	-12175
chr2	238886907	238887414	E067	-11395
chr2	238888018	238888228	E067	-10581
chr2	238888415	238888465	E067	-10344
chr2	238888921	238888998	E067	-9811
chr2	238889558	238889737	E067	-9072
chr2	238889976	238890179	E067	-8630
chr2	238893121	238893238	E067	-5571
chr2	238904560	238904874	E067	5751
chr2	238904955	238905113	E067	6146
chr2	238917607	238917771	E067	18798
chr2	238931681	238931768	E067	32872
chr2	238851806	238851846	E068	-46963
chr2	238851954	238852295	E068	-46514
chr2	238877816	238878038	E068	-20771
chr2	238878398	238878539	E068	-20270
chr2	238878551	238878601	E068	-20208
chr2	238878666	238878738	E068	-20071
chr2	238879158	238879263	E068	-19546
chr2	238886584	238886634	E068	-12175
chr2	238886907	238887414	E068	-11395
chr2	238888018	238888228	E068	-10581
chr2	238888415	238888465	E068	-10344
chr2	238888921	238888998	E068	-9811
chr2	238889558	238889737	E068	-9072
chr2	238889976	238890179	E068	-8630
chr2	238892164	238892276	E068	-6533
chr2	238893121	238893238	E068	-5571
chr2	238877816	238878038	E069	-20771
chr2	238878398	238878539	E069	-20270
chr2	238878551	238878601	E069	-20208
chr2	238878666	238878738	E069	-20071
chr2	238886584	238886634	E069	-12175
chr2	238886907	238887414	E069	-11395
chr2	238888018	238888228	E069	-10581
chr2	238888921	238888998	E069	-9811
chr2	238889558	238889737	E069	-9072
chr2	238893121	238893238	E069	-5571
chr2	238904955	238905113	E069	6146
chr2	238918301	238918438	E069	19492
chr2	238919370	238919610	E069	20561
chr2	238919757	238919867	E069	20948
chr2	238928552	238929028	E069	29743
chr2	238886584	238886634	E070	-12175
chr2	238886907	238887414	E070	-11395
chr2	238888921	238888998	E070	-9811
chr2	238851806	238851846	E071	-46963
chr2	238851954	238852295	E071	-46514
chr2	238878666	238878738	E071	-20071
chr2	238879158	238879263	E071	-19546
chr2	238886011	238886062	E071	-12747
chr2	238886584	238886634	E071	-12175
chr2	238886907	238887414	E071	-11395
chr2	238888018	238888228	E071	-10581
chr2	238888415	238888465	E071	-10344
chr2	238888921	238888998	E071	-9811
chr2	238893121	238893238	E071	-5571
chr2	238917607	238917771	E071	18798
chr2	238917904	238917968	E071	19095
chr2	238918301	238918438	E071	19492
chr2	238919370	238919610	E071	20561
chr2	238919757	238919867	E071	20948
chr2	238867147	238867197	E072	-31612
chr2	238878551	238878601	E072	-20208
chr2	238886011	238886062	E072	-12747
chr2	238886584	238886634	E072	-12175
chr2	238886907	238887414	E072	-11395
chr2	238888018	238888228	E072	-10581
chr2	238888415	238888465	E072	-10344
chr2	238888921	238888998	E072	-9811
chr2	238889558	238889737	E072	-9072
chr2	238893121	238893238	E072	-5571
chr2	238917607	238917771	E072	18798
chr2	238878551	238878601	E073	-20208
chr2	238878666	238878738	E073	-20071
chr2	238886011	238886062	E073	-12747
chr2	238886584	238886634	E073	-12175
chr2	238886907	238887414	E073	-11395
chr2	238888018	238888228	E073	-10581
chr2	238888415	238888465	E073	-10344
chr2	238888921	238888998	E073	-9811
chr2	238889558	238889737	E073	-9072
chr2	238892164	238892276	E073	-6533
chr2	238893121	238893238	E073	-5571
chr2	238851954	238852295	E074	-46514
chr2	238878551	238878601	E074	-20208
chr2	238878666	238878738	E074	-20071
chr2	238879158	238879263	E074	-19546
chr2	238880434	238880549	E074	-18260
chr2	238880894	238880969	E074	-17840
chr2	238884641	238884818	E074	-13991
chr2	238886011	238886062	E074	-12747
chr2	238886584	238886634	E074	-12175
chr2	238886907	238887414	E074	-11395
chr2	238888921	238888998	E074	-9811
chr2	238889558	238889737	E074	-9072
chr2	238889976	238890179	E074	-8630
chr2	238893121	238893238	E074	-5571
chr2	238904560	238904874	E074	5751
chr2	238904955	238905113	E074	6146
chr2	238915164	238915422	E074	16355
chr2	238917607	238917771	E074	18798
chr2	238917904	238917968	E074	19095
chr2	238918301	238918438	E074	19492
chr2	238919370	238919610	E074	20561
chr2	238919757	238919867	E074	20948
chr2	238931681	238931768	E074	32872
chr2	238877816	238878038	E081	-20771
chr2	238878398	238878539	E081	-20270
chr2	238886907	238887414	E082	-11395

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-22705
chr2	238876111	238876550	E067	-22259
chr2	238864688	238864740	E068	-34069
chr2	238864741	238864973	E068	-33836
chr2	238865051	238865134	E068	-33675
chr2	238865144	238865248	E068	-33561
chr2	238874796	238876104	E068	-22705
chr2	238876111	238876550	E068	-22259
chr2	238865051	238865134	E069	-33675
chr2	238865144	238865248	E069	-33561
chr2	238874796	238876104	E069	-22705
chr2	238876111	238876550	E069	-22259
chr2	238864741	238864973	E070	-33836
chr2	238874796	238876104	E070	-22705
chr2	238876111	238876550	E070	-22259
chr2	238874796	238876104	E071	-22705
chr2	238876111	238876550	E071	-22259
chr2	238874796	238876104	E072	-22705
chr2	238876111	238876550	E072	-22259
chr2	238865051	238865134	E073	-33675
chr2	238865144	238865248	E073	-33561
chr2	238874796	238876104	E073	-22705
chr2	238876111	238876550	E073	-22259
chr2	238874796	238876104	E074	-22705
chr2	238876111	238876550	E074	-22259
chr2	238876111	238876550	E081	-22259
chr2	238864688	238864740	E082	-34069
chr2	238864741	238864973	E082	-33836
chr2	238865051	238865134	E082	-33675
chr2	238865144	238865248	E082	-33561
chr2	238874796	238876104	E082	-22705
chr2	238876111	238876550	E082	-22259