rs10048814

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0128 (3837/29974,GnomAD)
C==0134 (3912/29118,TOPMED)
C==0152 (760/5008,1000G)
C==0177 (682/3854,ALSPAC)
C==0190 (705/3708,TWINSUK)

Position: chr2:237989113 (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.237989113C>T
GRCh37.p13 chr 2	NC_000002.11:g.238897755C>T

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	C=0.099	T=0.901
1000Genomes	American	Sub	694	C=0.180	T=0.820
1000Genomes	East Asian	Sub	1008	C=0.030	T=0.970
1000Genomes	Europe	Sub	1006	C=0.164	T=0.836
1000Genomes	Global	Study-wide	5008	C=0.152	T=0.848
1000Genomes	South Asian	Sub	978	C=0.310	T=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.177	T=0.823
The Genome Aggregation Database	African	Sub	8724	C=0.108	T=0.892
The Genome Aggregation Database	American	Sub	836	C=0.170	T=0.830
The Genome Aggregation Database	East Asian	Sub	1618	C=0.030	T=0.970
The Genome Aggregation Database	Europe	Sub	18494	C=0.144	T=0.856
The Genome Aggregation Database	Global	Study-wide	29974	C=0.128	T=0.872
The Genome Aggregation Database	Other	Sub	302	C=0.110	T=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.134	T=0.865
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.190	T=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
rs10048814	0.000146	alcohol consumption	23743675

eQTL of rs10048814 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238897755	SCLY	ENSG00000132330.12	C>T	7.8532e-10	-71775	Cerebellum
Chr2:238897755	SCLY	ENSG00000132330.12	C>T	1.0714e-8	-71775	Cortex
Chr2:238897755	SCLY	ENSG00000132330.12	C>T	2.0850e-8	-71775	Cerebellar_Hemisphere
Chr2:238897755	SCLY	ENSG00000132330.12	C>T	1.4177e-3	-71775	Caudate_basal_ganglia
Chr2:238897755	SCLY	ENSG00000132330.12	C>T	2.3006e-3	-71775	Substantia_nigra
Chr2:238897755	SCLY	ENSG00000132330.12	C>T	7.2091e-4	-71775	Anterior_cingulate_cortex

meQTL of rs10048814 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	-19717
chr2	238878398	238878539	E067	-19216
chr2	238878551	238878601	E067	-19154
chr2	238878666	238878738	E067	-19017
chr2	238879158	238879263	E067	-18492
chr2	238886584	238886634	E067	-11121
chr2	238886907	238887414	E067	-10341
chr2	238888018	238888228	E067	-9527
chr2	238888415	238888465	E067	-9290
chr2	238888921	238888998	E067	-8757
chr2	238889558	238889737	E067	-8018
chr2	238889976	238890179	E067	-7576
chr2	238893121	238893238	E067	-4517
chr2	238904560	238904874	E067	6805
chr2	238904955	238905113	E067	7200
chr2	238917607	238917771	E067	19852
chr2	238931681	238931768	E067	33926
chr2	238851806	238851846	E068	-45909
chr2	238851954	238852295	E068	-45460
chr2	238877816	238878038	E068	-19717
chr2	238878398	238878539	E068	-19216
chr2	238878551	238878601	E068	-19154
chr2	238878666	238878738	E068	-19017
chr2	238879158	238879263	E068	-18492
chr2	238886584	238886634	E068	-11121
chr2	238886907	238887414	E068	-10341
chr2	238888018	238888228	E068	-9527
chr2	238888415	238888465	E068	-9290
chr2	238888921	238888998	E068	-8757
chr2	238889558	238889737	E068	-8018
chr2	238889976	238890179	E068	-7576
chr2	238892164	238892276	E068	-5479
chr2	238893121	238893238	E068	-4517
chr2	238877816	238878038	E069	-19717
chr2	238878398	238878539	E069	-19216
chr2	238878551	238878601	E069	-19154
chr2	238878666	238878738	E069	-19017
chr2	238886584	238886634	E069	-11121
chr2	238886907	238887414	E069	-10341
chr2	238888018	238888228	E069	-9527
chr2	238888921	238888998	E069	-8757
chr2	238889558	238889737	E069	-8018
chr2	238893121	238893238	E069	-4517
chr2	238904955	238905113	E069	7200
chr2	238918301	238918438	E069	20546
chr2	238919370	238919610	E069	21615
chr2	238919757	238919867	E069	22002
chr2	238928552	238929028	E069	30797
chr2	238886584	238886634	E070	-11121
chr2	238886907	238887414	E070	-10341
chr2	238888921	238888998	E070	-8757
chr2	238851806	238851846	E071	-45909
chr2	238851954	238852295	E071	-45460
chr2	238878666	238878738	E071	-19017
chr2	238879158	238879263	E071	-18492
chr2	238886011	238886062	E071	-11693
chr2	238886584	238886634	E071	-11121
chr2	238886907	238887414	E071	-10341
chr2	238888018	238888228	E071	-9527
chr2	238888415	238888465	E071	-9290
chr2	238888921	238888998	E071	-8757
chr2	238893121	238893238	E071	-4517
chr2	238917607	238917771	E071	19852
chr2	238917904	238917968	E071	20149
chr2	238918301	238918438	E071	20546
chr2	238919370	238919610	E071	21615
chr2	238919757	238919867	E071	22002
chr2	238867147	238867197	E072	-30558
chr2	238878551	238878601	E072	-19154
chr2	238886011	238886062	E072	-11693
chr2	238886584	238886634	E072	-11121
chr2	238886907	238887414	E072	-10341
chr2	238888018	238888228	E072	-9527
chr2	238888415	238888465	E072	-9290
chr2	238888921	238888998	E072	-8757
chr2	238889558	238889737	E072	-8018
chr2	238893121	238893238	E072	-4517
chr2	238917607	238917771	E072	19852
chr2	238878551	238878601	E073	-19154
chr2	238878666	238878738	E073	-19017
chr2	238886011	238886062	E073	-11693
chr2	238886584	238886634	E073	-11121
chr2	238886907	238887414	E073	-10341
chr2	238888018	238888228	E073	-9527
chr2	238888415	238888465	E073	-9290
chr2	238888921	238888998	E073	-8757
chr2	238889558	238889737	E073	-8018
chr2	238892164	238892276	E073	-5479
chr2	238893121	238893238	E073	-4517
chr2	238851954	238852295	E074	-45460
chr2	238878551	238878601	E074	-19154
chr2	238878666	238878738	E074	-19017
chr2	238879158	238879263	E074	-18492
chr2	238880434	238880549	E074	-17206
chr2	238880894	238880969	E074	-16786
chr2	238884641	238884818	E074	-12937
chr2	238886011	238886062	E074	-11693
chr2	238886584	238886634	E074	-11121
chr2	238886907	238887414	E074	-10341
chr2	238888921	238888998	E074	-8757
chr2	238889558	238889737	E074	-8018
chr2	238889976	238890179	E074	-7576
chr2	238893121	238893238	E074	-4517
chr2	238904560	238904874	E074	6805
chr2	238904955	238905113	E074	7200
chr2	238915164	238915422	E074	17409
chr2	238917607	238917771	E074	19852
chr2	238917904	238917968	E074	20149
chr2	238918301	238918438	E074	20546
chr2	238919370	238919610	E074	21615
chr2	238919757	238919867	E074	22002
chr2	238931681	238931768	E074	33926
chr2	238877816	238878038	E081	-19717
chr2	238878398	238878539	E081	-19216
chr2	238886907	238887414	E082	-10341

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-21651
chr2	238876111	238876550	E067	-21205
chr2	238864688	238864740	E068	-33015
chr2	238864741	238864973	E068	-32782
chr2	238865051	238865134	E068	-32621
chr2	238865144	238865248	E068	-32507
chr2	238874796	238876104	E068	-21651
chr2	238876111	238876550	E068	-21205
chr2	238865051	238865134	E069	-32621
chr2	238865144	238865248	E069	-32507
chr2	238874796	238876104	E069	-21651
chr2	238876111	238876550	E069	-21205
chr2	238864741	238864973	E070	-32782
chr2	238874796	238876104	E070	-21651
chr2	238876111	238876550	E070	-21205
chr2	238874796	238876104	E071	-21651
chr2	238876111	238876550	E071	-21205
chr2	238874796	238876104	E072	-21651
chr2	238876111	238876550	E072	-21205
chr2	238865051	238865134	E073	-32621
chr2	238865144	238865248	E073	-32507
chr2	238874796	238876104	E073	-21651
chr2	238876111	238876550	E073	-21205
chr2	238874796	238876104	E074	-21651
chr2	238876111	238876550	E074	-21205
chr2	238876111	238876550	E081	-21205
chr2	238864688	238864740	E082	-33015
chr2	238864741	238864973	E082	-32782
chr2	238865051	238865134	E082	-32621
chr2	238865144	238865248	E082	-32507
chr2	238874796	238876104	E082	-21651
chr2	238876111	238876550	E082	-21205