rs7594965

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0128 (3830/29898,GnomAD)
C==0134 (3916/29118,TOPMED)
C==0152 (761/5008,1000G)
C==0177 (681/3854,ALSPAC)
C==0190 (705/3708,TWINSUK)

Position: chr2:238002459 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 119 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.238002459C>A
GRCh37.p13 chr 2	NC_000002.11:g.238911101C>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	C=0.100	A=0.900
1000Genomes	American	Sub	694	C=0.180	A=0.820
1000Genomes	East Asian	Sub	1008	C=0.030	A=0.970
1000Genomes	Europe	Sub	1006	C=0.164	A=0.836
1000Genomes	Global	Study-wide	5008	C=0.152	A=0.848
1000Genomes	South Asian	Sub	978	C=0.310	A=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.177	A=0.823
The Genome Aggregation Database	African	Sub	8700	C=0.109	A=0.891
The Genome Aggregation Database	American	Sub	836	C=0.170	A=0.830
The Genome Aggregation Database	East Asian	Sub	1620	C=0.030	A=0.970
The Genome Aggregation Database	Europe	Sub	18442	C=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29898	C=0.128	A=0.871
The Genome Aggregation Database	Other	Sub	300	C=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.134	A=0.865
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=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
rs7594965	0.000143	alcohol consumption	23743675

eQTL of rs7594965 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238911101	SCLY	ENSG00000132330.12	C>A	7.8532e-10	-58429	Cerebellum
Chr2:238911101	SCLY	ENSG00000132330.12	C>A	1.0714e-8	-58429	Cortex
Chr2:238911101	SCLY	ENSG00000132330.12	C>A	2.0850e-8	-58429	Cerebellar_Hemisphere
Chr2:238911101	SCLY	ENSG00000132330.12	C>A	1.4177e-3	-58429	Caudate_basal_ganglia
Chr2:238911101	SCLY	ENSG00000132330.12	C>A	2.3006e-3	-58429	Substantia_nigra
Chr2:238911101	SCLY	ENSG00000132330.12	C>A	7.2091e-4	-58429	Anterior_cingulate_cortex

meQTL of rs7594965 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	-33063
chr2	238878398	238878539	E067	-32562
chr2	238878551	238878601	E067	-32500
chr2	238878666	238878738	E067	-32363
chr2	238879158	238879263	E067	-31838
chr2	238886584	238886634	E067	-24467
chr2	238886907	238887414	E067	-23687
chr2	238888018	238888228	E067	-22873
chr2	238888415	238888465	E067	-22636
chr2	238888921	238888998	E067	-22103
chr2	238889558	238889737	E067	-21364
chr2	238889976	238890179	E067	-20922
chr2	238893121	238893238	E067	-17863
chr2	238904560	238904874	E067	-6227
chr2	238904955	238905113	E067	-5988
chr2	238917607	238917771	E067	6506
chr2	238931681	238931768	E067	20580
chr2	238950342	238950447	E067	39241
chr2	238951505	238951913	E067	40404
chr2	238877816	238878038	E068	-33063
chr2	238878398	238878539	E068	-32562
chr2	238878551	238878601	E068	-32500
chr2	238878666	238878738	E068	-32363
chr2	238879158	238879263	E068	-31838
chr2	238886584	238886634	E068	-24467
chr2	238886907	238887414	E068	-23687
chr2	238888018	238888228	E068	-22873
chr2	238888415	238888465	E068	-22636
chr2	238888921	238888998	E068	-22103
chr2	238889558	238889737	E068	-21364
chr2	238889976	238890179	E068	-20922
chr2	238892164	238892276	E068	-18825
chr2	238893121	238893238	E068	-17863
chr2	238877816	238878038	E069	-33063
chr2	238878398	238878539	E069	-32562
chr2	238878551	238878601	E069	-32500
chr2	238878666	238878738	E069	-32363
chr2	238886584	238886634	E069	-24467
chr2	238886907	238887414	E069	-23687
chr2	238888018	238888228	E069	-22873
chr2	238888921	238888998	E069	-22103
chr2	238889558	238889737	E069	-21364
chr2	238893121	238893238	E069	-17863
chr2	238904955	238905113	E069	-5988
chr2	238918301	238918438	E069	7200
chr2	238919370	238919610	E069	8269
chr2	238919757	238919867	E069	8656
chr2	238928552	238929028	E069	17451
chr2	238951505	238951913	E069	40404
chr2	238886584	238886634	E070	-24467
chr2	238886907	238887414	E070	-23687
chr2	238888921	238888998	E070	-22103
chr2	238878666	238878738	E071	-32363
chr2	238879158	238879263	E071	-31838
chr2	238886011	238886062	E071	-25039
chr2	238886584	238886634	E071	-24467
chr2	238886907	238887414	E071	-23687
chr2	238888018	238888228	E071	-22873
chr2	238888415	238888465	E071	-22636
chr2	238888921	238888998	E071	-22103
chr2	238893121	238893238	E071	-17863
chr2	238917607	238917771	E071	6506
chr2	238917904	238917968	E071	6803
chr2	238918301	238918438	E071	7200
chr2	238919370	238919610	E071	8269
chr2	238919757	238919867	E071	8656
chr2	238950342	238950447	E071	39241
chr2	238951505	238951913	E071	40404
chr2	238951961	238952020	E071	40860
chr2	238867147	238867197	E072	-43904
chr2	238878551	238878601	E072	-32500
chr2	238886011	238886062	E072	-25039
chr2	238886584	238886634	E072	-24467
chr2	238886907	238887414	E072	-23687
chr2	238888018	238888228	E072	-22873
chr2	238888415	238888465	E072	-22636
chr2	238888921	238888998	E072	-22103
chr2	238889558	238889737	E072	-21364
chr2	238893121	238893238	E072	-17863
chr2	238917607	238917771	E072	6506
chr2	238950342	238950447	E072	39241
chr2	238878551	238878601	E073	-32500
chr2	238878666	238878738	E073	-32363
chr2	238886011	238886062	E073	-25039
chr2	238886584	238886634	E073	-24467
chr2	238886907	238887414	E073	-23687
chr2	238888018	238888228	E073	-22873
chr2	238888415	238888465	E073	-22636
chr2	238888921	238888998	E073	-22103
chr2	238889558	238889737	E073	-21364
chr2	238892164	238892276	E073	-18825
chr2	238893121	238893238	E073	-17863
chr2	238878551	238878601	E074	-32500
chr2	238878666	238878738	E074	-32363
chr2	238879158	238879263	E074	-31838
chr2	238880434	238880549	E074	-30552
chr2	238880894	238880969	E074	-30132
chr2	238884641	238884818	E074	-26283
chr2	238886011	238886062	E074	-25039
chr2	238886584	238886634	E074	-24467
chr2	238886907	238887414	E074	-23687
chr2	238888921	238888998	E074	-22103
chr2	238889558	238889737	E074	-21364
chr2	238889976	238890179	E074	-20922
chr2	238893121	238893238	E074	-17863
chr2	238904560	238904874	E074	-6227
chr2	238904955	238905113	E074	-5988
chr2	238915164	238915422	E074	4063
chr2	238917607	238917771	E074	6506
chr2	238917904	238917968	E074	6803
chr2	238918301	238918438	E074	7200
chr2	238919370	238919610	E074	8269
chr2	238919757	238919867	E074	8656
chr2	238931681	238931768	E074	20580
chr2	238950342	238950447	E074	39241
chr2	238951505	238951913	E074	40404
chr2	238877816	238878038	E081	-33063
chr2	238878398	238878539	E081	-32562
chr2	238886907	238887414	E082	-23687

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-34997
chr2	238876111	238876550	E067	-34551
chr2	238864688	238864740	E068	-46361
chr2	238864741	238864973	E068	-46128
chr2	238865051	238865134	E068	-45967
chr2	238865144	238865248	E068	-45853
chr2	238874796	238876104	E068	-34997
chr2	238876111	238876550	E068	-34551
chr2	238865051	238865134	E069	-45967
chr2	238865144	238865248	E069	-45853
chr2	238874796	238876104	E069	-34997
chr2	238876111	238876550	E069	-34551
chr2	238864741	238864973	E070	-46128
chr2	238874796	238876104	E070	-34997
chr2	238876111	238876550	E070	-34551
chr2	238874796	238876104	E071	-34997
chr2	238876111	238876550	E071	-34551
chr2	238874796	238876104	E072	-34997
chr2	238876111	238876550	E072	-34551
chr2	238865051	238865134	E073	-45967
chr2	238865144	238865248	E073	-45853
chr2	238874796	238876104	E073	-34997
chr2	238876111	238876550	E073	-34551
chr2	238874796	238876104	E074	-34997
chr2	238876111	238876550	E074	-34551
chr2	238876111	238876550	E081	-34551
chr2	238864688	238864740	E082	-46361
chr2	238864741	238864973	E082	-46128
chr2	238865051	238865134	E082	-45967
chr2	238865144	238865248	E082	-45853
chr2	238874796	238876104	E082	-34997
chr2	238876111	238876550	E082	-34551