rs10929255

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==0186 (5578/29956,GnomAD)
G==0210 (6134/29118,TOPMED)
G==0254 (1273/5008,1000G)
G==0179 (688/3854,ALSPAC)
G==0191 (709/3708,TWINSUK)

Position: chr2:237970660 (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.237970660G>A
GRCh37.p13 chr 2	NC_000002.11:g.238879302G>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=0.289	A=0.711
1000Genomes	American	Sub	694	G=0.200	A=0.800
1000Genomes	East Asian	Sub	1008	G=0.231	A=0.769
1000Genomes	Europe	Sub	1006	G=0.167	A=0.833
1000Genomes	Global	Study-wide	5008	G=0.254	A=0.746
1000Genomes	South Asian	Sub	978	G=0.360	A=0.640
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.179	A=0.821
The Genome Aggregation Database	African	Sub	8712	G=0.265	A=0.735
The Genome Aggregation Database	American	Sub	838	G=0.190	A=0.810
The Genome Aggregation Database	East Asian	Sub	1614	G=0.234	A=0.766
The Genome Aggregation Database	Europe	Sub	18490	G=0.146	A=0.854
The Genome Aggregation Database	Global	Study-wide	29956	G=0.186	A=0.813
The Genome Aggregation Database	Other	Sub	302	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.210	A=0.789
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.191	A=0.809

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
rs10929255	0.000134	alcohol consumption	23743675

eQTL of rs10929255 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238879302	SCLY	ENSG00000132330.12	G>A	7.8532e-10	-90228	Cerebellum
Chr2:238879302	SCLY	ENSG00000132330.12	G>A	1.0714e-8	-90228	Cortex
Chr2:238879302	SCLY	ENSG00000132330.12	G>A	2.0850e-8	-90228	Cerebellar_Hemisphere
Chr2:238879302	SCLY	ENSG00000132330.12	G>A	2.3006e-3	-90228	Substantia_nigra
Chr2:238879302	SCLY	ENSG00000132330.12	G>A	7.2091e-4	-90228	Anterior_cingulate_cortex

meQTL of rs10929255 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0531652091525395	1.2398e-10

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	-44885
chr2	238877816	238878038	E067	-1264
chr2	238878398	238878539	E067	-763
chr2	238878551	238878601	E067	-701
chr2	238878666	238878738	E067	-564
chr2	238879158	238879263	E067	-39
chr2	238886584	238886634	E067	7282
chr2	238886907	238887414	E067	7605
chr2	238888018	238888228	E067	8716
chr2	238888415	238888465	E067	9113
chr2	238888921	238888998	E067	9619
chr2	238889558	238889737	E067	10256
chr2	238889976	238890179	E067	10674
chr2	238893121	238893238	E067	13819
chr2	238904560	238904874	E067	25258
chr2	238904955	238905113	E067	25653
chr2	238917607	238917771	E067	38305
chr2	238851806	238851846	E068	-27456
chr2	238851954	238852295	E068	-27007
chr2	238877816	238878038	E068	-1264
chr2	238878398	238878539	E068	-763
chr2	238878551	238878601	E068	-701
chr2	238878666	238878738	E068	-564
chr2	238879158	238879263	E068	-39
chr2	238886584	238886634	E068	7282
chr2	238886907	238887414	E068	7605
chr2	238888018	238888228	E068	8716
chr2	238888415	238888465	E068	9113
chr2	238888921	238888998	E068	9619
chr2	238889558	238889737	E068	10256
chr2	238889976	238890179	E068	10674
chr2	238892164	238892276	E068	12862
chr2	238893121	238893238	E068	13819
chr2	238840070	238840408	E069	-38894
chr2	238877816	238878038	E069	-1264
chr2	238878398	238878539	E069	-763
chr2	238878551	238878601	E069	-701
chr2	238878666	238878738	E069	-564
chr2	238886584	238886634	E069	7282
chr2	238886907	238887414	E069	7605
chr2	238888018	238888228	E069	8716
chr2	238888921	238888998	E069	9619
chr2	238889558	238889737	E069	10256
chr2	238893121	238893238	E069	13819
chr2	238904955	238905113	E069	25653
chr2	238918301	238918438	E069	38999
chr2	238919370	238919610	E069	40068
chr2	238919757	238919867	E069	40455
chr2	238928552	238929028	E069	49250
chr2	238886584	238886634	E070	7282
chr2	238886907	238887414	E070	7605
chr2	238888921	238888998	E070	9619
chr2	238840070	238840408	E071	-38894
chr2	238851806	238851846	E071	-27456
chr2	238851954	238852295	E071	-27007
chr2	238878666	238878738	E071	-564
chr2	238879158	238879263	E071	-39
chr2	238886011	238886062	E071	6709
chr2	238886584	238886634	E071	7282
chr2	238886907	238887414	E071	7605
chr2	238888018	238888228	E071	8716
chr2	238888415	238888465	E071	9113
chr2	238888921	238888998	E071	9619
chr2	238893121	238893238	E071	13819
chr2	238917607	238917771	E071	38305
chr2	238917904	238917968	E071	38602
chr2	238918301	238918438	E071	38999
chr2	238919370	238919610	E071	40068
chr2	238919757	238919867	E071	40455
chr2	238867147	238867197	E072	-12105
chr2	238878551	238878601	E072	-701
chr2	238886011	238886062	E072	6709
chr2	238886584	238886634	E072	7282
chr2	238886907	238887414	E072	7605
chr2	238888018	238888228	E072	8716
chr2	238888415	238888465	E072	9113
chr2	238888921	238888998	E072	9619
chr2	238889558	238889737	E072	10256
chr2	238893121	238893238	E072	13819
chr2	238917607	238917771	E072	38305
chr2	238840070	238840408	E073	-38894
chr2	238878551	238878601	E073	-701
chr2	238878666	238878738	E073	-564
chr2	238886011	238886062	E073	6709
chr2	238886584	238886634	E073	7282
chr2	238886907	238887414	E073	7605
chr2	238888018	238888228	E073	8716
chr2	238888415	238888465	E073	9113
chr2	238888921	238888998	E073	9619
chr2	238889558	238889737	E073	10256
chr2	238892164	238892276	E073	12862
chr2	238893121	238893238	E073	13819
chr2	238840070	238840408	E074	-38894
chr2	238851954	238852295	E074	-27007
chr2	238878551	238878601	E074	-701
chr2	238878666	238878738	E074	-564
chr2	238879158	238879263	E074	-39
chr2	238880434	238880549	E074	1132
chr2	238880894	238880969	E074	1592
chr2	238884641	238884818	E074	5339
chr2	238886011	238886062	E074	6709
chr2	238886584	238886634	E074	7282
chr2	238886907	238887414	E074	7605
chr2	238888921	238888998	E074	9619
chr2	238889558	238889737	E074	10256
chr2	238889976	238890179	E074	10674
chr2	238893121	238893238	E074	13819
chr2	238904560	238904874	E074	25258
chr2	238904955	238905113	E074	25653
chr2	238915164	238915422	E074	35862
chr2	238917607	238917771	E074	38305
chr2	238917904	238917968	E074	38602
chr2	238918301	238918438	E074	38999
chr2	238919370	238919610	E074	40068
chr2	238919757	238919867	E074	40455
chr2	238877816	238878038	E081	-1264
chr2	238878398	238878539	E081	-763
chr2	238886907	238887414	E082	7605

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-3198
chr2	238876111	238876550	E067	-2752
chr2	238864688	238864740	E068	-14562
chr2	238864741	238864973	E068	-14329
chr2	238865051	238865134	E068	-14168
chr2	238865144	238865248	E068	-14054
chr2	238874796	238876104	E068	-3198
chr2	238876111	238876550	E068	-2752
chr2	238865051	238865134	E069	-14168
chr2	238865144	238865248	E069	-14054
chr2	238874796	238876104	E069	-3198
chr2	238876111	238876550	E069	-2752
chr2	238864741	238864973	E070	-14329
chr2	238874796	238876104	E070	-3198
chr2	238876111	238876550	E070	-2752
chr2	238874796	238876104	E071	-3198
chr2	238876111	238876550	E071	-2752
chr2	238874796	238876104	E072	-3198
chr2	238876111	238876550	E072	-2752
chr2	238865051	238865134	E073	-14168
chr2	238865144	238865248	E073	-14054
chr2	238874796	238876104	E073	-3198
chr2	238876111	238876550	E073	-2752
chr2	238874796	238876104	E074	-3198
chr2	238876111	238876550	E074	-2752
chr2	238876111	238876550	E081	-2752
chr2	238864688	238864740	E082	-14562
chr2	238864741	238864973	E082	-14329
chr2	238865051	238865134	E082	-14168
chr2	238865144	238865248	E082	-14054
chr2	238874796	238876104	E082	-3198
chr2	238876111	238876550	E082	-2752