rs7567199

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==0143 (4285/29948,GnomAD)
G==0156 (4559/29118,TOPMED)
G==0168 (840/5008,1000G)
G==0176 (680/3854,ALSPAC)
G==0190 (705/3708,TWINSUK)

Position: chr2:237971888 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 118 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.237971888G>A
GRCh37.p13 chr 2	NC_000002.11:g.238880530G>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=0.160	A=0.840
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=0.168	A=0.832
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=0.176	A=0.824
The Genome Aggregation Database	African	Sub	8714	G=0.160	A=0.840
The Genome Aggregation Database	American	Sub	836	G=0.180	A=0.820
The Genome Aggregation Database	East Asian	Sub	1618	G=0.030	A=0.970
The Genome Aggregation Database	Europe	Sub	18478	G=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29948	G=0.143	A=0.856
The Genome Aggregation Database	Other	Sub	302	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.156	A=0.843
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
rs7567199	0.000141	alcohol consumption	23743675

eQTL of rs7567199 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238880530	SCLY	ENSG00000132330.12	G>A	7.8532e-10	-89000	Cerebellum
Chr2:238880530	SCLY	ENSG00000132330.12	G>A	1.0714e-8	-89000	Cortex
Chr2:238880530	SCLY	ENSG00000132330.12	G>A	2.0850e-8	-89000	Cerebellar_Hemisphere
Chr2:238880530	SCLY	ENSG00000132330.12	G>A	1.4177e-3	-89000	Caudate_basal_ganglia
Chr2:238880530	SCLY	ENSG00000132330.12	G>A	2.3006e-3	-89000	Substantia_nigra
Chr2:238880530	SCLY	ENSG00000132330.12	G>A	7.2091e-4	-89000	Anterior_cingulate_cortex

meQTL of rs7567199 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0595216574305454	1.4425e-12

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	238834367	238834417	E067	-46113
chr2	238877816	238878038	E067	-2492
chr2	238878398	238878539	E067	-1991
chr2	238878551	238878601	E067	-1929
chr2	238878666	238878738	E067	-1792
chr2	238879158	238879263	E067	-1267
chr2	238886584	238886634	E067	6054
chr2	238886907	238887414	E067	6377
chr2	238888018	238888228	E067	7488
chr2	238888415	238888465	E067	7885
chr2	238888921	238888998	E067	8391
chr2	238889558	238889737	E067	9028
chr2	238889976	238890179	E067	9446
chr2	238893121	238893238	E067	12591
chr2	238904560	238904874	E067	24030
chr2	238904955	238905113	E067	24425
chr2	238917607	238917771	E067	37077
chr2	238851806	238851846	E068	-28684
chr2	238851954	238852295	E068	-28235
chr2	238877816	238878038	E068	-2492
chr2	238878398	238878539	E068	-1991
chr2	238878551	238878601	E068	-1929
chr2	238878666	238878738	E068	-1792
chr2	238879158	238879263	E068	-1267
chr2	238886584	238886634	E068	6054
chr2	238886907	238887414	E068	6377
chr2	238888018	238888228	E068	7488
chr2	238888415	238888465	E068	7885
chr2	238888921	238888998	E068	8391
chr2	238889558	238889737	E068	9028
chr2	238889976	238890179	E068	9446
chr2	238892164	238892276	E068	11634
chr2	238893121	238893238	E068	12591
chr2	238840070	238840408	E069	-40122
chr2	238877816	238878038	E069	-2492
chr2	238878398	238878539	E069	-1991
chr2	238878551	238878601	E069	-1929
chr2	238878666	238878738	E069	-1792
chr2	238886584	238886634	E069	6054
chr2	238886907	238887414	E069	6377
chr2	238888018	238888228	E069	7488
chr2	238888921	238888998	E069	8391
chr2	238889558	238889737	E069	9028
chr2	238893121	238893238	E069	12591
chr2	238904955	238905113	E069	24425
chr2	238918301	238918438	E069	37771
chr2	238919370	238919610	E069	38840
chr2	238919757	238919867	E069	39227
chr2	238928552	238929028	E069	48022
chr2	238886584	238886634	E070	6054
chr2	238886907	238887414	E070	6377
chr2	238888921	238888998	E070	8391
chr2	238840070	238840408	E071	-40122
chr2	238851806	238851846	E071	-28684
chr2	238851954	238852295	E071	-28235
chr2	238878666	238878738	E071	-1792
chr2	238879158	238879263	E071	-1267
chr2	238886011	238886062	E071	5481
chr2	238886584	238886634	E071	6054
chr2	238886907	238887414	E071	6377
chr2	238888018	238888228	E071	7488
chr2	238888415	238888465	E071	7885
chr2	238888921	238888998	E071	8391
chr2	238893121	238893238	E071	12591
chr2	238917607	238917771	E071	37077
chr2	238917904	238917968	E071	37374
chr2	238918301	238918438	E071	37771
chr2	238919370	238919610	E071	38840
chr2	238919757	238919867	E071	39227
chr2	238867147	238867197	E072	-13333
chr2	238878551	238878601	E072	-1929
chr2	238886011	238886062	E072	5481
chr2	238886584	238886634	E072	6054
chr2	238886907	238887414	E072	6377
chr2	238888018	238888228	E072	7488
chr2	238888415	238888465	E072	7885
chr2	238888921	238888998	E072	8391
chr2	238889558	238889737	E072	9028
chr2	238893121	238893238	E072	12591
chr2	238917607	238917771	E072	37077
chr2	238840070	238840408	E073	-40122
chr2	238878551	238878601	E073	-1929
chr2	238878666	238878738	E073	-1792
chr2	238886011	238886062	E073	5481
chr2	238886584	238886634	E073	6054
chr2	238886907	238887414	E073	6377
chr2	238888018	238888228	E073	7488
chr2	238888415	238888465	E073	7885
chr2	238888921	238888998	E073	8391
chr2	238889558	238889737	E073	9028
chr2	238892164	238892276	E073	11634
chr2	238893121	238893238	E073	12591
chr2	238840070	238840408	E074	-40122
chr2	238851954	238852295	E074	-28235
chr2	238878551	238878601	E074	-1929
chr2	238878666	238878738	E074	-1792
chr2	238879158	238879263	E074	-1267
chr2	238880434	238880549	E074	0
chr2	238880894	238880969	E074	364
chr2	238884641	238884818	E074	4111
chr2	238886011	238886062	E074	5481
chr2	238886584	238886634	E074	6054
chr2	238886907	238887414	E074	6377
chr2	238888921	238888998	E074	8391
chr2	238889558	238889737	E074	9028
chr2	238889976	238890179	E074	9446
chr2	238893121	238893238	E074	12591
chr2	238904560	238904874	E074	24030
chr2	238904955	238905113	E074	24425
chr2	238915164	238915422	E074	34634
chr2	238917607	238917771	E074	37077
chr2	238917904	238917968	E074	37374
chr2	238918301	238918438	E074	37771
chr2	238919370	238919610	E074	38840
chr2	238919757	238919867	E074	39227
chr2	238877816	238878038	E081	-2492
chr2	238878398	238878539	E081	-1991
chr2	238886907	238887414	E082	6377

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-4426
chr2	238876111	238876550	E067	-3980
chr2	238864688	238864740	E068	-15790
chr2	238864741	238864973	E068	-15557
chr2	238865051	238865134	E068	-15396
chr2	238865144	238865248	E068	-15282
chr2	238874796	238876104	E068	-4426
chr2	238876111	238876550	E068	-3980
chr2	238865051	238865134	E069	-15396
chr2	238865144	238865248	E069	-15282
chr2	238874796	238876104	E069	-4426
chr2	238876111	238876550	E069	-3980
chr2	238864741	238864973	E070	-15557
chr2	238874796	238876104	E070	-4426
chr2	238876111	238876550	E070	-3980
chr2	238874796	238876104	E071	-4426
chr2	238876111	238876550	E071	-3980
chr2	238874796	238876104	E072	-4426
chr2	238876111	238876550	E072	-3980
chr2	238865051	238865134	E073	-15396
chr2	238865144	238865248	E073	-15282
chr2	238874796	238876104	E073	-4426
chr2	238876111	238876550	E073	-3980
chr2	238874796	238876104	E074	-4426
chr2	238876111	238876550	E074	-3980
chr2	238876111	238876550	E081	-3980
chr2	238864688	238864740	E082	-15790
chr2	238864741	238864973	E082	-15557
chr2	238865051	238865134	E082	-15396
chr2	238865144	238865248	E082	-15282
chr2	238874796	238876104	E082	-4426
chr2	238876111	238876550	E082	-3980