rs6431570

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==0128 (3854/29902,GnomAD)
G==0135 (3954/29118,TOPMED)
G==0152 (762/5008,1000G)
G==0177 (682/3854,ALSPAC)
G==0190 (704/3708,TWINSUK)

Position: chr2:238015926 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 124 Enhancers around

Promoter: 29 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238015926G>A
GRCh37.p13 chr 2	NC_000002.11:g.238924568G>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=0.101	A=0.899
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=0.163	A=0.837
1000Genomes	Global	Study-wide	5008	G=0.152	A=0.848
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=0.177	A=0.823
The Genome Aggregation Database	African	Sub	8700	G=0.111	A=0.889
The Genome Aggregation Database	American	Sub	836	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	18442	G=0.144	A=0.855
The Genome Aggregation Database	Global	Study-wide	29902	G=0.128	A=0.871
The Genome Aggregation Database	Other	Sub	302	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.135	A=0.864
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
rs6431570	0.000153	alcohol consumption	23743675

eQTL of rs6431570 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238924568	SCLY	ENSG00000132330.12	G>A	7.8532e-10	-44962	Cerebellum
Chr2:238924568	SCLY	ENSG00000132330.12	G>A	1.0714e-8	-44962	Cortex
Chr2:238924568	SCLY	ENSG00000132330.12	G>A	2.0850e-8	-44962	Cerebellar_Hemisphere
Chr2:238924568	SCLY	ENSG00000132330.12	G>A	1.4177e-3	-44962	Caudate_basal_ganglia
Chr2:238924568	SCLY	ENSG00000132330.12	G>A	2.3006e-3	-44962	Substantia_nigra
Chr2:238924568	SCLY	ENSG00000132330.12	G>A	7.2091e-4	-44962	Anterior_cingulate_cortex

meQTL of rs6431570 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0655561838740832	8.8573e-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	238877816	238878038	E067	-46530
chr2	238878398	238878539	E067	-46029
chr2	238878551	238878601	E067	-45967
chr2	238878666	238878738	E067	-45830
chr2	238879158	238879263	E067	-45305
chr2	238886584	238886634	E067	-37934
chr2	238886907	238887414	E067	-37154
chr2	238888018	238888228	E067	-36340
chr2	238888415	238888465	E067	-36103
chr2	238888921	238888998	E067	-35570
chr2	238889558	238889737	E067	-34831
chr2	238889976	238890179	E067	-34389
chr2	238893121	238893238	E067	-31330
chr2	238904560	238904874	E067	-19694
chr2	238904955	238905113	E067	-19455
chr2	238917607	238917771	E067	-6797
chr2	238931681	238931768	E067	7113
chr2	238950342	238950447	E067	25774
chr2	238951505	238951913	E067	26937
chr2	238970839	238970899	E067	46271
chr2	238877816	238878038	E068	-46530
chr2	238878398	238878539	E068	-46029
chr2	238878551	238878601	E068	-45967
chr2	238878666	238878738	E068	-45830
chr2	238879158	238879263	E068	-45305
chr2	238886584	238886634	E068	-37934
chr2	238886907	238887414	E068	-37154
chr2	238888018	238888228	E068	-36340
chr2	238888415	238888465	E068	-36103
chr2	238888921	238888998	E068	-35570
chr2	238889558	238889737	E068	-34831
chr2	238889976	238890179	E068	-34389
chr2	238892164	238892276	E068	-32292
chr2	238893121	238893238	E068	-31330
chr2	238970839	238970899	E068	46271
chr2	238877816	238878038	E069	-46530
chr2	238878398	238878539	E069	-46029
chr2	238878551	238878601	E069	-45967
chr2	238878666	238878738	E069	-45830
chr2	238886584	238886634	E069	-37934
chr2	238886907	238887414	E069	-37154
chr2	238888018	238888228	E069	-36340
chr2	238888921	238888998	E069	-35570
chr2	238889558	238889737	E069	-34831
chr2	238893121	238893238	E069	-31330
chr2	238904955	238905113	E069	-19455
chr2	238918301	238918438	E069	-6130
chr2	238919370	238919610	E069	-4958
chr2	238919757	238919867	E069	-4701
chr2	238928552	238929028	E069	3984
chr2	238951505	238951913	E069	26937
chr2	238970839	238970899	E069	46271
chr2	238886584	238886634	E070	-37934
chr2	238886907	238887414	E070	-37154
chr2	238888921	238888998	E070	-35570
chr2	238970839	238970899	E070	46271
chr2	238878666	238878738	E071	-45830
chr2	238879158	238879263	E071	-45305
chr2	238886011	238886062	E071	-38506
chr2	238886584	238886634	E071	-37934
chr2	238886907	238887414	E071	-37154
chr2	238888018	238888228	E071	-36340
chr2	238888415	238888465	E071	-36103
chr2	238888921	238888998	E071	-35570
chr2	238893121	238893238	E071	-31330
chr2	238917607	238917771	E071	-6797
chr2	238917904	238917968	E071	-6600
chr2	238918301	238918438	E071	-6130
chr2	238919370	238919610	E071	-4958
chr2	238919757	238919867	E071	-4701
chr2	238950342	238950447	E071	25774
chr2	238951505	238951913	E071	26937
chr2	238951961	238952020	E071	27393
chr2	238970839	238970899	E071	46271
chr2	238878551	238878601	E072	-45967
chr2	238886011	238886062	E072	-38506
chr2	238886584	238886634	E072	-37934
chr2	238886907	238887414	E072	-37154
chr2	238888018	238888228	E072	-36340
chr2	238888415	238888465	E072	-36103
chr2	238888921	238888998	E072	-35570
chr2	238889558	238889737	E072	-34831
chr2	238893121	238893238	E072	-31330
chr2	238917607	238917771	E072	-6797
chr2	238950342	238950447	E072	25774
chr2	238878551	238878601	E073	-45967
chr2	238878666	238878738	E073	-45830
chr2	238886011	238886062	E073	-38506
chr2	238886584	238886634	E073	-37934
chr2	238886907	238887414	E073	-37154
chr2	238888018	238888228	E073	-36340
chr2	238888415	238888465	E073	-36103
chr2	238888921	238888998	E073	-35570
chr2	238889558	238889737	E073	-34831
chr2	238892164	238892276	E073	-32292
chr2	238893121	238893238	E073	-31330
chr2	238970839	238970899	E073	46271
chr2	238878551	238878601	E074	-45967
chr2	238878666	238878738	E074	-45830
chr2	238879158	238879263	E074	-45305
chr2	238880434	238880549	E074	-44019
chr2	238880894	238880969	E074	-43599
chr2	238884641	238884818	E074	-39750
chr2	238886011	238886062	E074	-38506
chr2	238886584	238886634	E074	-37934
chr2	238886907	238887414	E074	-37154
chr2	238888921	238888998	E074	-35570
chr2	238889558	238889737	E074	-34831
chr2	238889976	238890179	E074	-34389
chr2	238893121	238893238	E074	-31330
chr2	238904560	238904874	E074	-19694
chr2	238904955	238905113	E074	-19455
chr2	238915164	238915422	E074	-9146
chr2	238917607	238917771	E074	-6797
chr2	238917904	238917968	E074	-6600
chr2	238918301	238918438	E074	-6130
chr2	238919370	238919610	E074	-4958
chr2	238919757	238919867	E074	-4701
chr2	238931681	238931768	E074	7113
chr2	238950342	238950447	E074	25774
chr2	238951505	238951913	E074	26937
chr2	238877816	238878038	E081	-46530
chr2	238878398	238878539	E081	-46029
chr2	238886907	238887414	E082	-37154

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-48464
chr2	238876111	238876550	E067	-48018
chr2	238968700	238970607	E067	44132
chr2	238874796	238876104	E068	-48464
chr2	238876111	238876550	E068	-48018
chr2	238968700	238970607	E068	44132
chr2	238874796	238876104	E069	-48464
chr2	238876111	238876550	E069	-48018
chr2	238968700	238970607	E069	44132
chr2	238874796	238876104	E070	-48464
chr2	238876111	238876550	E070	-48018
chr2	238968700	238970607	E070	44132
chr2	238874796	238876104	E071	-48464
chr2	238876111	238876550	E071	-48018
chr2	238968700	238970607	E071	44132
chr2	238874796	238876104	E072	-48464
chr2	238876111	238876550	E072	-48018
chr2	238968700	238970607	E072	44132
chr2	238874796	238876104	E073	-48464
chr2	238876111	238876550	E073	-48018
chr2	238968700	238970607	E073	44132
chr2	238874796	238876104	E074	-48464
chr2	238876111	238876550	E074	-48018
chr2	238968700	238970607	E074	44132
chr2	238876111	238876550	E081	-48018
chr2	238968700	238970607	E081	44132
chr2	238874796	238876104	E082	-48464
chr2	238876111	238876550	E082	-48018
chr2	238968700	238970607	E082	44132