rs1446924

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 (3659/29964,GnomAD)
A==0125 (3651/29118,TOPMED)
A==0143 (715/5008,1000G)
A==0176 (679/3854,ALSPAC)
A==0190 (704/3708,TWINSUK)

Position: chr2:237969098 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 117 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.237969098A>G
GRCh37.p13 chr 2	NC_000002.11:g.238877740A>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

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	8718	A=0.088	G=0.912
The Genome Aggregation Database	American	Sub	836	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	18486	A=0.143	G=0.856
The Genome Aggregation Database	Global	Study-wide	29964	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

SNP ID	p-value	Traits	Study
rs1446924	0.000133	alcohol consumption	23743675

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238877740	SCLY	ENSG00000132330.12	A>G	7.8532e-10	-91790	Cerebellum
Chr2:238877740	SCLY	ENSG00000132330.12	A>G	1.0714e-8	-91790	Cortex
Chr2:238877740	SCLY	ENSG00000132330.12	A>G	2.0850e-8	-91790	Cerebellar_Hemisphere
Chr2:238877740	SCLY	ENSG00000132330.12	A>G	1.4177e-3	-91790	Caudate_basal_ganglia
Chr2:238877740	SCLY	ENSG00000132330.12	A>G	2.3006e-3	-91790	Substantia_nigra
Chr2:238877740	SCLY	ENSG00000132330.12	A>G	7.2091e-4	-91790	Anterior_cingulate_cortex

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	-43323
chr2	238877816	238878038	E067	76
chr2	238878398	238878539	E067	658
chr2	238878551	238878601	E067	811
chr2	238878666	238878738	E067	926
chr2	238879158	238879263	E067	1418
chr2	238886584	238886634	E067	8844
chr2	238886907	238887414	E067	9167
chr2	238888018	238888228	E067	10278
chr2	238888415	238888465	E067	10675
chr2	238888921	238888998	E067	11181
chr2	238889558	238889737	E067	11818
chr2	238889976	238890179	E067	12236
chr2	238893121	238893238	E067	15381
chr2	238904560	238904874	E067	26820
chr2	238904955	238905113	E067	27215
chr2	238917607	238917771	E067	39867
chr2	238851806	238851846	E068	-25894
chr2	238851954	238852295	E068	-25445
chr2	238877816	238878038	E068	76
chr2	238878398	238878539	E068	658
chr2	238878551	238878601	E068	811
chr2	238878666	238878738	E068	926
chr2	238879158	238879263	E068	1418
chr2	238886584	238886634	E068	8844
chr2	238886907	238887414	E068	9167
chr2	238888018	238888228	E068	10278
chr2	238888415	238888465	E068	10675
chr2	238888921	238888998	E068	11181
chr2	238889558	238889737	E068	11818
chr2	238889976	238890179	E068	12236
chr2	238892164	238892276	E068	14424
chr2	238893121	238893238	E068	15381
chr2	238840070	238840408	E069	-37332
chr2	238877816	238878038	E069	76
chr2	238878398	238878539	E069	658
chr2	238878551	238878601	E069	811
chr2	238878666	238878738	E069	926
chr2	238886584	238886634	E069	8844
chr2	238886907	238887414	E069	9167
chr2	238888018	238888228	E069	10278
chr2	238888921	238888998	E069	11181
chr2	238889558	238889737	E069	11818
chr2	238893121	238893238	E069	15381
chr2	238904955	238905113	E069	27215
chr2	238918301	238918438	E069	40561
chr2	238919370	238919610	E069	41630
chr2	238919757	238919867	E069	42017
chr2	238886584	238886634	E070	8844
chr2	238886907	238887414	E070	9167
chr2	238888921	238888998	E070	11181
chr2	238840070	238840408	E071	-37332
chr2	238851806	238851846	E071	-25894
chr2	238851954	238852295	E071	-25445
chr2	238878666	238878738	E071	926
chr2	238879158	238879263	E071	1418
chr2	238886011	238886062	E071	8271
chr2	238886584	238886634	E071	8844
chr2	238886907	238887414	E071	9167
chr2	238888018	238888228	E071	10278
chr2	238888415	238888465	E071	10675
chr2	238888921	238888998	E071	11181
chr2	238893121	238893238	E071	15381
chr2	238917607	238917771	E071	39867
chr2	238917904	238917968	E071	40164
chr2	238918301	238918438	E071	40561
chr2	238919370	238919610	E071	41630
chr2	238919757	238919867	E071	42017
chr2	238867147	238867197	E072	-10543
chr2	238878551	238878601	E072	811
chr2	238886011	238886062	E072	8271
chr2	238886584	238886634	E072	8844
chr2	238886907	238887414	E072	9167
chr2	238888018	238888228	E072	10278
chr2	238888415	238888465	E072	10675
chr2	238888921	238888998	E072	11181
chr2	238889558	238889737	E072	11818
chr2	238893121	238893238	E072	15381
chr2	238917607	238917771	E072	39867
chr2	238840070	238840408	E073	-37332
chr2	238878551	238878601	E073	811
chr2	238878666	238878738	E073	926
chr2	238886011	238886062	E073	8271
chr2	238886584	238886634	E073	8844
chr2	238886907	238887414	E073	9167
chr2	238888018	238888228	E073	10278
chr2	238888415	238888465	E073	10675
chr2	238888921	238888998	E073	11181
chr2	238889558	238889737	E073	11818
chr2	238892164	238892276	E073	14424
chr2	238893121	238893238	E073	15381
chr2	238840070	238840408	E074	-37332
chr2	238851954	238852295	E074	-25445
chr2	238878551	238878601	E074	811
chr2	238878666	238878738	E074	926
chr2	238879158	238879263	E074	1418
chr2	238880434	238880549	E074	2694
chr2	238880894	238880969	E074	3154
chr2	238884641	238884818	E074	6901
chr2	238886011	238886062	E074	8271
chr2	238886584	238886634	E074	8844
chr2	238886907	238887414	E074	9167
chr2	238888921	238888998	E074	11181
chr2	238889558	238889737	E074	11818
chr2	238889976	238890179	E074	12236
chr2	238893121	238893238	E074	15381
chr2	238904560	238904874	E074	26820
chr2	238904955	238905113	E074	27215
chr2	238915164	238915422	E074	37424
chr2	238917607	238917771	E074	39867
chr2	238917904	238917968	E074	40164
chr2	238918301	238918438	E074	40561
chr2	238919370	238919610	E074	41630
chr2	238919757	238919867	E074	42017
chr2	238877816	238878038	E081	76
chr2	238878398	238878539	E081	658
chr2	238886907	238887414	E082	9167

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-1636
chr2	238876111	238876550	E067	-1190
chr2	238864688	238864740	E068	-13000
chr2	238864741	238864973	E068	-12767
chr2	238865051	238865134	E068	-12606
chr2	238865144	238865248	E068	-12492
chr2	238874796	238876104	E068	-1636
chr2	238876111	238876550	E068	-1190
chr2	238865051	238865134	E069	-12606
chr2	238865144	238865248	E069	-12492
chr2	238874796	238876104	E069	-1636
chr2	238876111	238876550	E069	-1190
chr2	238864741	238864973	E070	-12767
chr2	238874796	238876104	E070	-1636
chr2	238876111	238876550	E070	-1190
chr2	238874796	238876104	E071	-1636
chr2	238876111	238876550	E071	-1190
chr2	238874796	238876104	E072	-1636
chr2	238876111	238876550	E072	-1190
chr2	238865051	238865134	E073	-12606
chr2	238865144	238865248	E073	-12492
chr2	238874796	238876104	E073	-1636
chr2	238876111	238876550	E073	-1190
chr2	238874796	238876104	E074	-1636
chr2	238876111	238876550	E074	-1190
chr2	238876111	238876550	E081	-1190
chr2	238864688	238864740	E082	-13000
chr2	238864741	238864973	E082	-12767
chr2	238865051	238865134	E082	-12606
chr2	238865144	238865248	E082	-12492
chr2	238874796	238876104	E082	-1636
chr2	238876111	238876550	E082	-1190

rs1446924

Genomic Coordinates

Gene: UBE2F, ubiquitin conjugating enzyme E2 F (putative)(plus strand)

Gene: UBE2F-SCLY, UBE2F-SCLY readthrough (NMD candidate)(plus strand)

Population Frequency

P-Value

eQTL of rs1446924 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs1446924 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)