rs4461215

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==0122 (3641/29852,GnomAD)
G==0125 (3646/29118,TOPMED)
G==0143 (717/5008,1000G)
G==0176 (679/3854,ALSPAC)
G==0190 (706/3708,TWINSUK)

Position: chr2:237975324 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 120 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.237975324G>A
GRCh37.p13 chr 2	NC_000002.11:g.238883966G>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=0.070	A=0.930
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=0.143	A=0.857
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	8704	G=0.089	A=0.911
The Genome Aggregation Database	American	Sub	838	G=0.170	A=0.830
The Genome Aggregation Database	East Asian	Sub	1622	G=0.030	A=0.970
The Genome Aggregation Database	Europe	Sub	18386	G=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29852	G=0.122	A=0.878
The Genome Aggregation Database	Other	Sub	302	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.125	A=0.874
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
rs4461215	0.000152	alcohol consumption	23743675

eQTL of rs4461215 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238883966	SCLY	ENSG00000132330.12	G>A	7.8532e-10	-85564	Cerebellum
Chr2:238883966	SCLY	ENSG00000132330.12	G>A	1.0714e-8	-85564	Cortex
Chr2:238883966	SCLY	ENSG00000132330.12	G>A	2.0850e-8	-85564	Cerebellar_Hemisphere
Chr2:238883966	SCLY	ENSG00000132330.12	G>A	1.4177e-3	-85564	Caudate_basal_ganglia
Chr2:238883966	SCLY	ENSG00000132330.12	G>A	2.3006e-3	-85564	Substantia_nigra
Chr2:238883966	SCLY	ENSG00000132330.12	G>A	7.2091e-4	-85564	Anterior_cingulate_cortex

meQTL of rs4461215 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0667011901921593	3.7259e-15

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	-49549
chr2	238877816	238878038	E067	-5928
chr2	238878398	238878539	E067	-5427
chr2	238878551	238878601	E067	-5365
chr2	238878666	238878738	E067	-5228
chr2	238879158	238879263	E067	-4703
chr2	238886584	238886634	E067	2618
chr2	238886907	238887414	E067	2941
chr2	238888018	238888228	E067	4052
chr2	238888415	238888465	E067	4449
chr2	238888921	238888998	E067	4955
chr2	238889558	238889737	E067	5592
chr2	238889976	238890179	E067	6010
chr2	238893121	238893238	E067	9155
chr2	238904560	238904874	E067	20594
chr2	238904955	238905113	E067	20989
chr2	238917607	238917771	E067	33641
chr2	238931681	238931768	E067	47715
chr2	238851806	238851846	E068	-32120
chr2	238851954	238852295	E068	-31671
chr2	238877816	238878038	E068	-5928
chr2	238878398	238878539	E068	-5427
chr2	238878551	238878601	E068	-5365
chr2	238878666	238878738	E068	-5228
chr2	238879158	238879263	E068	-4703
chr2	238886584	238886634	E068	2618
chr2	238886907	238887414	E068	2941
chr2	238888018	238888228	E068	4052
chr2	238888415	238888465	E068	4449
chr2	238888921	238888998	E068	4955
chr2	238889558	238889737	E068	5592
chr2	238889976	238890179	E068	6010
chr2	238892164	238892276	E068	8198
chr2	238893121	238893238	E068	9155
chr2	238840070	238840408	E069	-43558
chr2	238877816	238878038	E069	-5928
chr2	238878398	238878539	E069	-5427
chr2	238878551	238878601	E069	-5365
chr2	238878666	238878738	E069	-5228
chr2	238886584	238886634	E069	2618
chr2	238886907	238887414	E069	2941
chr2	238888018	238888228	E069	4052
chr2	238888921	238888998	E069	4955
chr2	238889558	238889737	E069	5592
chr2	238893121	238893238	E069	9155
chr2	238904955	238905113	E069	20989
chr2	238918301	238918438	E069	34335
chr2	238919370	238919610	E069	35404
chr2	238919757	238919867	E069	35791
chr2	238928552	238929028	E069	44586
chr2	238886584	238886634	E070	2618
chr2	238886907	238887414	E070	2941
chr2	238888921	238888998	E070	4955
chr2	238840070	238840408	E071	-43558
chr2	238851806	238851846	E071	-32120
chr2	238851954	238852295	E071	-31671
chr2	238878666	238878738	E071	-5228
chr2	238879158	238879263	E071	-4703
chr2	238886011	238886062	E071	2045
chr2	238886584	238886634	E071	2618
chr2	238886907	238887414	E071	2941
chr2	238888018	238888228	E071	4052
chr2	238888415	238888465	E071	4449
chr2	238888921	238888998	E071	4955
chr2	238893121	238893238	E071	9155
chr2	238917607	238917771	E071	33641
chr2	238917904	238917968	E071	33938
chr2	238918301	238918438	E071	34335
chr2	238919370	238919610	E071	35404
chr2	238919757	238919867	E071	35791
chr2	238867147	238867197	E072	-16769
chr2	238878551	238878601	E072	-5365
chr2	238886011	238886062	E072	2045
chr2	238886584	238886634	E072	2618
chr2	238886907	238887414	E072	2941
chr2	238888018	238888228	E072	4052
chr2	238888415	238888465	E072	4449
chr2	238888921	238888998	E072	4955
chr2	238889558	238889737	E072	5592
chr2	238893121	238893238	E072	9155
chr2	238917607	238917771	E072	33641
chr2	238840070	238840408	E073	-43558
chr2	238878551	238878601	E073	-5365
chr2	238878666	238878738	E073	-5228
chr2	238886011	238886062	E073	2045
chr2	238886584	238886634	E073	2618
chr2	238886907	238887414	E073	2941
chr2	238888018	238888228	E073	4052
chr2	238888415	238888465	E073	4449
chr2	238888921	238888998	E073	4955
chr2	238889558	238889737	E073	5592
chr2	238892164	238892276	E073	8198
chr2	238893121	238893238	E073	9155
chr2	238840070	238840408	E074	-43558
chr2	238851954	238852295	E074	-31671
chr2	238878551	238878601	E074	-5365
chr2	238878666	238878738	E074	-5228
chr2	238879158	238879263	E074	-4703
chr2	238880434	238880549	E074	-3417
chr2	238880894	238880969	E074	-2997
chr2	238884641	238884818	E074	675
chr2	238886011	238886062	E074	2045
chr2	238886584	238886634	E074	2618
chr2	238886907	238887414	E074	2941
chr2	238888921	238888998	E074	4955
chr2	238889558	238889737	E074	5592
chr2	238889976	238890179	E074	6010
chr2	238893121	238893238	E074	9155
chr2	238904560	238904874	E074	20594
chr2	238904955	238905113	E074	20989
chr2	238915164	238915422	E074	31198
chr2	238917607	238917771	E074	33641
chr2	238917904	238917968	E074	33938
chr2	238918301	238918438	E074	34335
chr2	238919370	238919610	E074	35404
chr2	238919757	238919867	E074	35791
chr2	238931681	238931768	E074	47715
chr2	238877816	238878038	E081	-5928
chr2	238878398	238878539	E081	-5427
chr2	238886907	238887414	E082	2941

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-7862
chr2	238876111	238876550	E067	-7416
chr2	238864688	238864740	E068	-19226
chr2	238864741	238864973	E068	-18993
chr2	238865051	238865134	E068	-18832
chr2	238865144	238865248	E068	-18718
chr2	238874796	238876104	E068	-7862
chr2	238876111	238876550	E068	-7416
chr2	238865051	238865134	E069	-18832
chr2	238865144	238865248	E069	-18718
chr2	238874796	238876104	E069	-7862
chr2	238876111	238876550	E069	-7416
chr2	238864741	238864973	E070	-18993
chr2	238874796	238876104	E070	-7862
chr2	238876111	238876550	E070	-7416
chr2	238874796	238876104	E071	-7862
chr2	238876111	238876550	E071	-7416
chr2	238874796	238876104	E072	-7862
chr2	238876111	238876550	E072	-7416
chr2	238865051	238865134	E073	-18832
chr2	238865144	238865248	E073	-18718
chr2	238874796	238876104	E073	-7862
chr2	238876111	238876550	E073	-7416
chr2	238874796	238876104	E074	-7862
chr2	238876111	238876550	E074	-7416
chr2	238876111	238876550	E081	-7416
chr2	238864688	238864740	E082	-19226
chr2	238864741	238864973	E082	-18993
chr2	238865051	238865134	E082	-18832
chr2	238865144	238865248	E082	-18718
chr2	238874796	238876104	E082	-7862
chr2	238876111	238876550	E082	-7416