rs6726393

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0127 (3825/29942,GnomAD)
A==0134 (3911/29118,TOPMED)
A==0152 (759/5008,1000G)
A==0177 (682/3854,ALSPAC)
A==0190 (705/3708,TWINSUK)

Position: chr2:237982949 (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.237982949A>G
GRCh37.p13 chr 2	NC_000002.11:g.238891591A>G

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	A=0.098	G=0.902
1000Genomes	American	Sub	694	A=0.180	G=0.820
1000Genomes	East Asian	Sub	1008	A=0.030	G=0.970
1000Genomes	Europe	Sub	1006	A=0.164	G=0.836
1000Genomes	Global	Study-wide	5008	A=0.152	G=0.848
1000Genomes	South Asian	Sub	978	A=0.310	G=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.177	G=0.823
The Genome Aggregation Database	African	Sub	8714	A=0.108	G=0.892
The Genome Aggregation Database	American	Sub	838	A=0.170	G=0.830
The Genome Aggregation Database	East Asian	Sub	1622	A=0.030	G=0.970
The Genome Aggregation Database	Europe	Sub	18466	A=0.143	G=0.856
The Genome Aggregation Database	Global	Study-wide	29942	A=0.127	G=0.872
The Genome Aggregation Database	Other	Sub	302	A=0.110	G=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.134	G=0.865
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.190	G=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
rs6726393	0.000147	alcohol consumption	23743675

eQTL of rs6726393 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238891591	SCLY	ENSG00000132330.12	A>G	7.8532e-10	-77939	Cerebellum
Chr2:238891591	SCLY	ENSG00000132330.12	A>G	1.0714e-8	-77939	Cortex
Chr2:238891591	SCLY	ENSG00000132330.12	A>G	2.0850e-8	-77939	Cerebellar_Hemisphere
Chr2:238891591	SCLY	ENSG00000132330.12	A>G	1.4177e-3	-77939	Caudate_basal_ganglia
Chr2:238891591	SCLY	ENSG00000132330.12	A>G	2.3006e-3	-77939	Substantia_nigra
Chr2:238891591	SCLY	ENSG00000132330.12	A>G	7.2091e-4	-77939	Anterior_cingulate_cortex

meQTL of rs6726393 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	-13553
chr2	238878398	238878539	E067	-13052
chr2	238878551	238878601	E067	-12990
chr2	238878666	238878738	E067	-12853
chr2	238879158	238879263	E067	-12328
chr2	238886584	238886634	E067	-4957
chr2	238886907	238887414	E067	-4177
chr2	238888018	238888228	E067	-3363
chr2	238888415	238888465	E067	-3126
chr2	238888921	238888998	E067	-2593
chr2	238889558	238889737	E067	-1854
chr2	238889976	238890179	E067	-1412
chr2	238893121	238893238	E067	1530
chr2	238904560	238904874	E067	12969
chr2	238904955	238905113	E067	13364
chr2	238917607	238917771	E067	26016
chr2	238931681	238931768	E067	40090
chr2	238851806	238851846	E068	-39745
chr2	238851954	238852295	E068	-39296
chr2	238877816	238878038	E068	-13553
chr2	238878398	238878539	E068	-13052
chr2	238878551	238878601	E068	-12990
chr2	238878666	238878738	E068	-12853
chr2	238879158	238879263	E068	-12328
chr2	238886584	238886634	E068	-4957
chr2	238886907	238887414	E068	-4177
chr2	238888018	238888228	E068	-3363
chr2	238888415	238888465	E068	-3126
chr2	238888921	238888998	E068	-2593
chr2	238889558	238889737	E068	-1854
chr2	238889976	238890179	E068	-1412
chr2	238892164	238892276	E068	573
chr2	238893121	238893238	E068	1530
chr2	238877816	238878038	E069	-13553
chr2	238878398	238878539	E069	-13052
chr2	238878551	238878601	E069	-12990
chr2	238878666	238878738	E069	-12853
chr2	238886584	238886634	E069	-4957
chr2	238886907	238887414	E069	-4177
chr2	238888018	238888228	E069	-3363
chr2	238888921	238888998	E069	-2593
chr2	238889558	238889737	E069	-1854
chr2	238893121	238893238	E069	1530
chr2	238904955	238905113	E069	13364
chr2	238918301	238918438	E069	26710
chr2	238919370	238919610	E069	27779
chr2	238919757	238919867	E069	28166
chr2	238928552	238929028	E069	36961
chr2	238886584	238886634	E070	-4957
chr2	238886907	238887414	E070	-4177
chr2	238888921	238888998	E070	-2593
chr2	238851806	238851846	E071	-39745
chr2	238851954	238852295	E071	-39296
chr2	238878666	238878738	E071	-12853
chr2	238879158	238879263	E071	-12328
chr2	238886011	238886062	E071	-5529
chr2	238886584	238886634	E071	-4957
chr2	238886907	238887414	E071	-4177
chr2	238888018	238888228	E071	-3363
chr2	238888415	238888465	E071	-3126
chr2	238888921	238888998	E071	-2593
chr2	238893121	238893238	E071	1530
chr2	238917607	238917771	E071	26016
chr2	238917904	238917968	E071	26313
chr2	238918301	238918438	E071	26710
chr2	238919370	238919610	E071	27779
chr2	238919757	238919867	E071	28166
chr2	238867147	238867197	E072	-24394
chr2	238878551	238878601	E072	-12990
chr2	238886011	238886062	E072	-5529
chr2	238886584	238886634	E072	-4957
chr2	238886907	238887414	E072	-4177
chr2	238888018	238888228	E072	-3363
chr2	238888415	238888465	E072	-3126
chr2	238888921	238888998	E072	-2593
chr2	238889558	238889737	E072	-1854
chr2	238893121	238893238	E072	1530
chr2	238917607	238917771	E072	26016
chr2	238878551	238878601	E073	-12990
chr2	238878666	238878738	E073	-12853
chr2	238886011	238886062	E073	-5529
chr2	238886584	238886634	E073	-4957
chr2	238886907	238887414	E073	-4177
chr2	238888018	238888228	E073	-3363
chr2	238888415	238888465	E073	-3126
chr2	238888921	238888998	E073	-2593
chr2	238889558	238889737	E073	-1854
chr2	238892164	238892276	E073	573
chr2	238893121	238893238	E073	1530
chr2	238851954	238852295	E074	-39296
chr2	238878551	238878601	E074	-12990
chr2	238878666	238878738	E074	-12853
chr2	238879158	238879263	E074	-12328
chr2	238880434	238880549	E074	-11042
chr2	238880894	238880969	E074	-10622
chr2	238884641	238884818	E074	-6773
chr2	238886011	238886062	E074	-5529
chr2	238886584	238886634	E074	-4957
chr2	238886907	238887414	E074	-4177
chr2	238888921	238888998	E074	-2593
chr2	238889558	238889737	E074	-1854
chr2	238889976	238890179	E074	-1412
chr2	238893121	238893238	E074	1530
chr2	238904560	238904874	E074	12969
chr2	238904955	238905113	E074	13364
chr2	238915164	238915422	E074	23573
chr2	238917607	238917771	E074	26016
chr2	238917904	238917968	E074	26313
chr2	238918301	238918438	E074	26710
chr2	238919370	238919610	E074	27779
chr2	238919757	238919867	E074	28166
chr2	238931681	238931768	E074	40090
chr2	238877816	238878038	E081	-13553
chr2	238878398	238878539	E081	-13052
chr2	238886907	238887414	E082	-4177

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-15487
chr2	238876111	238876550	E067	-15041
chr2	238864688	238864740	E068	-26851
chr2	238864741	238864973	E068	-26618
chr2	238865051	238865134	E068	-26457
chr2	238865144	238865248	E068	-26343
chr2	238874796	238876104	E068	-15487
chr2	238876111	238876550	E068	-15041
chr2	238865051	238865134	E069	-26457
chr2	238865144	238865248	E069	-26343
chr2	238874796	238876104	E069	-15487
chr2	238876111	238876550	E069	-15041
chr2	238864741	238864973	E070	-26618
chr2	238874796	238876104	E070	-15487
chr2	238876111	238876550	E070	-15041
chr2	238874796	238876104	E071	-15487
chr2	238876111	238876550	E071	-15041
chr2	238874796	238876104	E072	-15487
chr2	238876111	238876550	E072	-15041
chr2	238865051	238865134	E073	-26457
chr2	238865144	238865248	E073	-26343
chr2	238874796	238876104	E073	-15487
chr2	238876111	238876550	E073	-15041
chr2	238874796	238876104	E074	-15487
chr2	238876111	238876550	E074	-15041
chr2	238876111	238876550	E081	-15041
chr2	238864688	238864740	E082	-26851
chr2	238864741	238864973	E082	-26618
chr2	238865051	238865134	E082	-26457
chr2	238865144	238865248	E082	-26343
chr2	238874796	238876104	E082	-15487
chr2	238876111	238876550	E082	-15041