rs6711485

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==0122 (3657/29918,GnomAD)
A==0125 (3651/29118,TOPMED)
A==0143 (717/5008,1000G)
A==0176 (677/3854,ALSPAC)
A==0190 (705/3708,TWINSUK)

Position: chr2:237974033 (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.237974033A>G
GRCh37.p13 chr 2	NC_000002.11:g.238882675A>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=0.070	G=0.930
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=0.143	G=0.857
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=0.176	G=0.824
The Genome Aggregation Database	African	Sub	8720	A=0.089	G=0.911
The Genome Aggregation Database	American	Sub	836	A=0.170	G=0.830
The Genome Aggregation Database	East Asian	Sub	1620	A=0.030	G=0.970
The Genome Aggregation Database	Europe	Sub	18440	A=0.144	G=0.856
The Genome Aggregation Database	Global	Study-wide	29918	A=0.122	G=0.877
The Genome Aggregation Database	Other	Sub	302	A=0.110	G=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.125	G=0.874
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
rs6711485	0.000145	alcohol consumption	23743675

eQTL of rs6711485 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238882675	SCLY	ENSG00000132330.12	A>G	7.8532e-10	-86855	Cerebellum
Chr2:238882675	SCLY	ENSG00000132330.12	A>G	1.0714e-8	-86855	Cortex
Chr2:238882675	SCLY	ENSG00000132330.12	A>G	2.0850e-8	-86855	Cerebellar_Hemisphere
Chr2:238882675	SCLY	ENSG00000132330.12	A>G	7.2091e-4	-86855	Anterior_cingulate_cortex

meQTL of rs6711485 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	-48258
chr2	238877816	238878038	E067	-4637
chr2	238878398	238878539	E067	-4136
chr2	238878551	238878601	E067	-4074
chr2	238878666	238878738	E067	-3937
chr2	238879158	238879263	E067	-3412
chr2	238886584	238886634	E067	3909
chr2	238886907	238887414	E067	4232
chr2	238888018	238888228	E067	5343
chr2	238888415	238888465	E067	5740
chr2	238888921	238888998	E067	6246
chr2	238889558	238889737	E067	6883
chr2	238889976	238890179	E067	7301
chr2	238893121	238893238	E067	10446
chr2	238904560	238904874	E067	21885
chr2	238904955	238905113	E067	22280
chr2	238917607	238917771	E067	34932
chr2	238931681	238931768	E067	49006
chr2	238851806	238851846	E068	-30829
chr2	238851954	238852295	E068	-30380
chr2	238877816	238878038	E068	-4637
chr2	238878398	238878539	E068	-4136
chr2	238878551	238878601	E068	-4074
chr2	238878666	238878738	E068	-3937
chr2	238879158	238879263	E068	-3412
chr2	238886584	238886634	E068	3909
chr2	238886907	238887414	E068	4232
chr2	238888018	238888228	E068	5343
chr2	238888415	238888465	E068	5740
chr2	238888921	238888998	E068	6246
chr2	238889558	238889737	E068	6883
chr2	238889976	238890179	E068	7301
chr2	238892164	238892276	E068	9489
chr2	238893121	238893238	E068	10446
chr2	238840070	238840408	E069	-42267
chr2	238877816	238878038	E069	-4637
chr2	238878398	238878539	E069	-4136
chr2	238878551	238878601	E069	-4074
chr2	238878666	238878738	E069	-3937
chr2	238886584	238886634	E069	3909
chr2	238886907	238887414	E069	4232
chr2	238888018	238888228	E069	5343
chr2	238888921	238888998	E069	6246
chr2	238889558	238889737	E069	6883
chr2	238893121	238893238	E069	10446
chr2	238904955	238905113	E069	22280
chr2	238918301	238918438	E069	35626
chr2	238919370	238919610	E069	36695
chr2	238919757	238919867	E069	37082
chr2	238928552	238929028	E069	45877
chr2	238886584	238886634	E070	3909
chr2	238886907	238887414	E070	4232
chr2	238888921	238888998	E070	6246
chr2	238840070	238840408	E071	-42267
chr2	238851806	238851846	E071	-30829
chr2	238851954	238852295	E071	-30380
chr2	238878666	238878738	E071	-3937
chr2	238879158	238879263	E071	-3412
chr2	238886011	238886062	E071	3336
chr2	238886584	238886634	E071	3909
chr2	238886907	238887414	E071	4232
chr2	238888018	238888228	E071	5343
chr2	238888415	238888465	E071	5740
chr2	238888921	238888998	E071	6246
chr2	238893121	238893238	E071	10446
chr2	238917607	238917771	E071	34932
chr2	238917904	238917968	E071	35229
chr2	238918301	238918438	E071	35626
chr2	238919370	238919610	E071	36695
chr2	238919757	238919867	E071	37082
chr2	238867147	238867197	E072	-15478
chr2	238878551	238878601	E072	-4074
chr2	238886011	238886062	E072	3336
chr2	238886584	238886634	E072	3909
chr2	238886907	238887414	E072	4232
chr2	238888018	238888228	E072	5343
chr2	238888415	238888465	E072	5740
chr2	238888921	238888998	E072	6246
chr2	238889558	238889737	E072	6883
chr2	238893121	238893238	E072	10446
chr2	238917607	238917771	E072	34932
chr2	238840070	238840408	E073	-42267
chr2	238878551	238878601	E073	-4074
chr2	238878666	238878738	E073	-3937
chr2	238886011	238886062	E073	3336
chr2	238886584	238886634	E073	3909
chr2	238886907	238887414	E073	4232
chr2	238888018	238888228	E073	5343
chr2	238888415	238888465	E073	5740
chr2	238888921	238888998	E073	6246
chr2	238889558	238889737	E073	6883
chr2	238892164	238892276	E073	9489
chr2	238893121	238893238	E073	10446
chr2	238840070	238840408	E074	-42267
chr2	238851954	238852295	E074	-30380
chr2	238878551	238878601	E074	-4074
chr2	238878666	238878738	E074	-3937
chr2	238879158	238879263	E074	-3412
chr2	238880434	238880549	E074	-2126
chr2	238880894	238880969	E074	-1706
chr2	238884641	238884818	E074	1966
chr2	238886011	238886062	E074	3336
chr2	238886584	238886634	E074	3909
chr2	238886907	238887414	E074	4232
chr2	238888921	238888998	E074	6246
chr2	238889558	238889737	E074	6883
chr2	238889976	238890179	E074	7301
chr2	238893121	238893238	E074	10446
chr2	238904560	238904874	E074	21885
chr2	238904955	238905113	E074	22280
chr2	238915164	238915422	E074	32489
chr2	238917607	238917771	E074	34932
chr2	238917904	238917968	E074	35229
chr2	238918301	238918438	E074	35626
chr2	238919370	238919610	E074	36695
chr2	238919757	238919867	E074	37082
chr2	238931681	238931768	E074	49006
chr2	238877816	238878038	E081	-4637
chr2	238878398	238878539	E081	-4136
chr2	238886907	238887414	E082	4232

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-6571
chr2	238876111	238876550	E067	-6125
chr2	238864688	238864740	E068	-17935
chr2	238864741	238864973	E068	-17702
chr2	238865051	238865134	E068	-17541
chr2	238865144	238865248	E068	-17427
chr2	238874796	238876104	E068	-6571
chr2	238876111	238876550	E068	-6125
chr2	238865051	238865134	E069	-17541
chr2	238865144	238865248	E069	-17427
chr2	238874796	238876104	E069	-6571
chr2	238876111	238876550	E069	-6125
chr2	238864741	238864973	E070	-17702
chr2	238874796	238876104	E070	-6571
chr2	238876111	238876550	E070	-6125
chr2	238874796	238876104	E071	-6571
chr2	238876111	238876550	E071	-6125
chr2	238874796	238876104	E072	-6571
chr2	238876111	238876550	E072	-6125
chr2	238865051	238865134	E073	-17541
chr2	238865144	238865248	E073	-17427
chr2	238874796	238876104	E073	-6571
chr2	238876111	238876550	E073	-6125
chr2	238874796	238876104	E074	-6571
chr2	238876111	238876550	E074	-6125
chr2	238876111	238876550	E081	-6125
chr2	238864688	238864740	E082	-17935
chr2	238864741	238864973	E082	-17702
chr2	238865051	238865134	E082	-17541
chr2	238865144	238865248	E082	-17427
chr2	238874796	238876104	E082	-6571
chr2	238876111	238876550	E082	-6125