rs11692068

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==0127 (3828/29966,GnomAD)
C==0133 (3899/29118,TOPMED)
C==0151 (756/5008,1000G)
C==0177 (681/3854,ALSPAC)
C==0190 (705/3708,TWINSUK)

Position: chr2:237988964 (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.237988964C>T
GRCh37.p13 chr 2	NC_000002.11:g.238897606C>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=0.096	T=0.904
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=0.151	T=0.849
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	838	C=0.170	T=0.830
The Genome Aggregation Database	East Asian	Sub	1620	C=0.030	T=0.970
The Genome Aggregation Database	Europe	Sub	18482	C=0.143	T=0.856
The Genome Aggregation Database	Global	Study-wide	29966	C=0.127	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=0.133	T=0.866
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
rs11692068	0.000141	alcohol consumption	23743675

eQTL of rs11692068 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238897606	SCLY	ENSG00000132330.12	C>T	7.8532e-10	-71924	Cerebellum
Chr2:238897606	SCLY	ENSG00000132330.12	C>T	1.0714e-8	-71924	Cortex
Chr2:238897606	SCLY	ENSG00000132330.12	C>T	2.0850e-8	-71924	Cerebellar_Hemisphere
Chr2:238897606	SCLY	ENSG00000132330.12	C>T	1.4177e-3	-71924	Caudate_basal_ganglia
Chr2:238897606	SCLY	ENSG00000132330.12	C>T	2.3006e-3	-71924	Substantia_nigra
Chr2:238897606	SCLY	ENSG00000132330.12	C>T	7.2091e-4	-71924	Anterior_cingulate_cortex

meQTL of rs11692068 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	-19568
chr2	238878398	238878539	E067	-19067
chr2	238878551	238878601	E067	-19005
chr2	238878666	238878738	E067	-18868
chr2	238879158	238879263	E067	-18343
chr2	238886584	238886634	E067	-10972
chr2	238886907	238887414	E067	-10192
chr2	238888018	238888228	E067	-9378
chr2	238888415	238888465	E067	-9141
chr2	238888921	238888998	E067	-8608
chr2	238889558	238889737	E067	-7869
chr2	238889976	238890179	E067	-7427
chr2	238893121	238893238	E067	-4368
chr2	238904560	238904874	E067	6954
chr2	238904955	238905113	E067	7349
chr2	238917607	238917771	E067	20001
chr2	238931681	238931768	E067	34075
chr2	238851806	238851846	E068	-45760
chr2	238851954	238852295	E068	-45311
chr2	238877816	238878038	E068	-19568
chr2	238878398	238878539	E068	-19067
chr2	238878551	238878601	E068	-19005
chr2	238878666	238878738	E068	-18868
chr2	238879158	238879263	E068	-18343
chr2	238886584	238886634	E068	-10972
chr2	238886907	238887414	E068	-10192
chr2	238888018	238888228	E068	-9378
chr2	238888415	238888465	E068	-9141
chr2	238888921	238888998	E068	-8608
chr2	238889558	238889737	E068	-7869
chr2	238889976	238890179	E068	-7427
chr2	238892164	238892276	E068	-5330
chr2	238893121	238893238	E068	-4368
chr2	238877816	238878038	E069	-19568
chr2	238878398	238878539	E069	-19067
chr2	238878551	238878601	E069	-19005
chr2	238878666	238878738	E069	-18868
chr2	238886584	238886634	E069	-10972
chr2	238886907	238887414	E069	-10192
chr2	238888018	238888228	E069	-9378
chr2	238888921	238888998	E069	-8608
chr2	238889558	238889737	E069	-7869
chr2	238893121	238893238	E069	-4368
chr2	238904955	238905113	E069	7349
chr2	238918301	238918438	E069	20695
chr2	238919370	238919610	E069	21764
chr2	238919757	238919867	E069	22151
chr2	238928552	238929028	E069	30946
chr2	238886584	238886634	E070	-10972
chr2	238886907	238887414	E070	-10192
chr2	238888921	238888998	E070	-8608
chr2	238851806	238851846	E071	-45760
chr2	238851954	238852295	E071	-45311
chr2	238878666	238878738	E071	-18868
chr2	238879158	238879263	E071	-18343
chr2	238886011	238886062	E071	-11544
chr2	238886584	238886634	E071	-10972
chr2	238886907	238887414	E071	-10192
chr2	238888018	238888228	E071	-9378
chr2	238888415	238888465	E071	-9141
chr2	238888921	238888998	E071	-8608
chr2	238893121	238893238	E071	-4368
chr2	238917607	238917771	E071	20001
chr2	238917904	238917968	E071	20298
chr2	238918301	238918438	E071	20695
chr2	238919370	238919610	E071	21764
chr2	238919757	238919867	E071	22151
chr2	238867147	238867197	E072	-30409
chr2	238878551	238878601	E072	-19005
chr2	238886011	238886062	E072	-11544
chr2	238886584	238886634	E072	-10972
chr2	238886907	238887414	E072	-10192
chr2	238888018	238888228	E072	-9378
chr2	238888415	238888465	E072	-9141
chr2	238888921	238888998	E072	-8608
chr2	238889558	238889737	E072	-7869
chr2	238893121	238893238	E072	-4368
chr2	238917607	238917771	E072	20001
chr2	238878551	238878601	E073	-19005
chr2	238878666	238878738	E073	-18868
chr2	238886011	238886062	E073	-11544
chr2	238886584	238886634	E073	-10972
chr2	238886907	238887414	E073	-10192
chr2	238888018	238888228	E073	-9378
chr2	238888415	238888465	E073	-9141
chr2	238888921	238888998	E073	-8608
chr2	238889558	238889737	E073	-7869
chr2	238892164	238892276	E073	-5330
chr2	238893121	238893238	E073	-4368
chr2	238851954	238852295	E074	-45311
chr2	238878551	238878601	E074	-19005
chr2	238878666	238878738	E074	-18868
chr2	238879158	238879263	E074	-18343
chr2	238880434	238880549	E074	-17057
chr2	238880894	238880969	E074	-16637
chr2	238884641	238884818	E074	-12788
chr2	238886011	238886062	E074	-11544
chr2	238886584	238886634	E074	-10972
chr2	238886907	238887414	E074	-10192
chr2	238888921	238888998	E074	-8608
chr2	238889558	238889737	E074	-7869
chr2	238889976	238890179	E074	-7427
chr2	238893121	238893238	E074	-4368
chr2	238904560	238904874	E074	6954
chr2	238904955	238905113	E074	7349
chr2	238915164	238915422	E074	17558
chr2	238917607	238917771	E074	20001
chr2	238917904	238917968	E074	20298
chr2	238918301	238918438	E074	20695
chr2	238919370	238919610	E074	21764
chr2	238919757	238919867	E074	22151
chr2	238931681	238931768	E074	34075
chr2	238877816	238878038	E081	-19568
chr2	238878398	238878539	E081	-19067
chr2	238886907	238887414	E082	-10192

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-21502
chr2	238876111	238876550	E067	-21056
chr2	238864688	238864740	E068	-32866
chr2	238864741	238864973	E068	-32633
chr2	238865051	238865134	E068	-32472
chr2	238865144	238865248	E068	-32358
chr2	238874796	238876104	E068	-21502
chr2	238876111	238876550	E068	-21056
chr2	238865051	238865134	E069	-32472
chr2	238865144	238865248	E069	-32358
chr2	238874796	238876104	E069	-21502
chr2	238876111	238876550	E069	-21056
chr2	238864741	238864973	E070	-32633
chr2	238874796	238876104	E070	-21502
chr2	238876111	238876550	E070	-21056
chr2	238874796	238876104	E071	-21502
chr2	238876111	238876550	E071	-21056
chr2	238874796	238876104	E072	-21502
chr2	238876111	238876550	E072	-21056
chr2	238865051	238865134	E073	-32472
chr2	238865144	238865248	E073	-32358
chr2	238874796	238876104	E073	-21502
chr2	238876111	238876550	E073	-21056
chr2	238874796	238876104	E074	-21502
chr2	238876111	238876550	E074	-21056
chr2	238876111	238876550	E081	-21056
chr2	238864688	238864740	E082	-32866
chr2	238864741	238864973	E082	-32633
chr2	238865051	238865134	E082	-32472
chr2	238865144	238865248	E082	-32358
chr2	238874796	238876104	E082	-21502
chr2	238876111	238876550	E082	-21056