rs10166061

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 (3829/29988,GnomAD)
C==0134 (3909/29118,TOPMED)
C==0152 (760/5008,1000G)
C==0177 (682/3854,ALSPAC)
C==0190 (705/3708,TWINSUK)

Position: chr2:237997869 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 119 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.237997869C>T
GRCh37.p13 chr 2	NC_000002.11:g.238906511C>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=0.100	T=0.900
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	8728	C=0.107	T=0.893
The Genome Aggregation Database	American	Sub	838	C=0.170	T=0.830
The Genome Aggregation Database	East Asian	Sub	1622	C=0.030	T=0.970
The Genome Aggregation Database	Europe	Sub	18498	C=0.144	T=0.856
The Genome Aggregation Database	Global	Study-wide	29988	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=0.134	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
rs10166061	0.000149	alcohol consumption	23743675

eQTL of rs10166061 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238906511	SCLY	ENSG00000132330.12	C>T	7.8532e-10	-63019	Cerebellum
Chr2:238906511	SCLY	ENSG00000132330.12	C>T	1.0714e-8	-63019	Cortex
Chr2:238906511	SCLY	ENSG00000132330.12	C>T	2.0850e-8	-63019	Cerebellar_Hemisphere
Chr2:238906511	SCLY	ENSG00000132330.12	C>T	1.4177e-3	-63019	Caudate_basal_ganglia
Chr2:238906511	SCLY	ENSG00000132330.12	C>T	2.3006e-3	-63019	Substantia_nigra
Chr2:238906511	SCLY	ENSG00000132330.12	C>T	7.2091e-4	-63019	Anterior_cingulate_cortex

meQTL of rs10166061 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	-28473
chr2	238878398	238878539	E067	-27972
chr2	238878551	238878601	E067	-27910
chr2	238878666	238878738	E067	-27773
chr2	238879158	238879263	E067	-27248
chr2	238886584	238886634	E067	-19877
chr2	238886907	238887414	E067	-19097
chr2	238888018	238888228	E067	-18283
chr2	238888415	238888465	E067	-18046
chr2	238888921	238888998	E067	-17513
chr2	238889558	238889737	E067	-16774
chr2	238889976	238890179	E067	-16332
chr2	238893121	238893238	E067	-13273
chr2	238904560	238904874	E067	-1637
chr2	238904955	238905113	E067	-1398
chr2	238917607	238917771	E067	11096
chr2	238931681	238931768	E067	25170
chr2	238950342	238950447	E067	43831
chr2	238951505	238951913	E067	44994
chr2	238877816	238878038	E068	-28473
chr2	238878398	238878539	E068	-27972
chr2	238878551	238878601	E068	-27910
chr2	238878666	238878738	E068	-27773
chr2	238879158	238879263	E068	-27248
chr2	238886584	238886634	E068	-19877
chr2	238886907	238887414	E068	-19097
chr2	238888018	238888228	E068	-18283
chr2	238888415	238888465	E068	-18046
chr2	238888921	238888998	E068	-17513
chr2	238889558	238889737	E068	-16774
chr2	238889976	238890179	E068	-16332
chr2	238892164	238892276	E068	-14235
chr2	238893121	238893238	E068	-13273
chr2	238877816	238878038	E069	-28473
chr2	238878398	238878539	E069	-27972
chr2	238878551	238878601	E069	-27910
chr2	238878666	238878738	E069	-27773
chr2	238886584	238886634	E069	-19877
chr2	238886907	238887414	E069	-19097
chr2	238888018	238888228	E069	-18283
chr2	238888921	238888998	E069	-17513
chr2	238889558	238889737	E069	-16774
chr2	238893121	238893238	E069	-13273
chr2	238904955	238905113	E069	-1398
chr2	238918301	238918438	E069	11790
chr2	238919370	238919610	E069	12859
chr2	238919757	238919867	E069	13246
chr2	238928552	238929028	E069	22041
chr2	238951505	238951913	E069	44994
chr2	238886584	238886634	E070	-19877
chr2	238886907	238887414	E070	-19097
chr2	238888921	238888998	E070	-17513
chr2	238878666	238878738	E071	-27773
chr2	238879158	238879263	E071	-27248
chr2	238886011	238886062	E071	-20449
chr2	238886584	238886634	E071	-19877
chr2	238886907	238887414	E071	-19097
chr2	238888018	238888228	E071	-18283
chr2	238888415	238888465	E071	-18046
chr2	238888921	238888998	E071	-17513
chr2	238893121	238893238	E071	-13273
chr2	238917607	238917771	E071	11096
chr2	238917904	238917968	E071	11393
chr2	238918301	238918438	E071	11790
chr2	238919370	238919610	E071	12859
chr2	238919757	238919867	E071	13246
chr2	238950342	238950447	E071	43831
chr2	238951505	238951913	E071	44994
chr2	238951961	238952020	E071	45450
chr2	238867147	238867197	E072	-39314
chr2	238878551	238878601	E072	-27910
chr2	238886011	238886062	E072	-20449
chr2	238886584	238886634	E072	-19877
chr2	238886907	238887414	E072	-19097
chr2	238888018	238888228	E072	-18283
chr2	238888415	238888465	E072	-18046
chr2	238888921	238888998	E072	-17513
chr2	238889558	238889737	E072	-16774
chr2	238893121	238893238	E072	-13273
chr2	238917607	238917771	E072	11096
chr2	238950342	238950447	E072	43831
chr2	238878551	238878601	E073	-27910
chr2	238878666	238878738	E073	-27773
chr2	238886011	238886062	E073	-20449
chr2	238886584	238886634	E073	-19877
chr2	238886907	238887414	E073	-19097
chr2	238888018	238888228	E073	-18283
chr2	238888415	238888465	E073	-18046
chr2	238888921	238888998	E073	-17513
chr2	238889558	238889737	E073	-16774
chr2	238892164	238892276	E073	-14235
chr2	238893121	238893238	E073	-13273
chr2	238878551	238878601	E074	-27910
chr2	238878666	238878738	E074	-27773
chr2	238879158	238879263	E074	-27248
chr2	238880434	238880549	E074	-25962
chr2	238880894	238880969	E074	-25542
chr2	238884641	238884818	E074	-21693
chr2	238886011	238886062	E074	-20449
chr2	238886584	238886634	E074	-19877
chr2	238886907	238887414	E074	-19097
chr2	238888921	238888998	E074	-17513
chr2	238889558	238889737	E074	-16774
chr2	238889976	238890179	E074	-16332
chr2	238893121	238893238	E074	-13273
chr2	238904560	238904874	E074	-1637
chr2	238904955	238905113	E074	-1398
chr2	238915164	238915422	E074	8653
chr2	238917607	238917771	E074	11096
chr2	238917904	238917968	E074	11393
chr2	238918301	238918438	E074	11790
chr2	238919370	238919610	E074	12859
chr2	238919757	238919867	E074	13246
chr2	238931681	238931768	E074	25170
chr2	238950342	238950447	E074	43831
chr2	238951505	238951913	E074	44994
chr2	238877816	238878038	E081	-28473
chr2	238878398	238878539	E081	-27972
chr2	238886907	238887414	E082	-19097

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-30407
chr2	238876111	238876550	E067	-29961
chr2	238864688	238864740	E068	-41771
chr2	238864741	238864973	E068	-41538
chr2	238865051	238865134	E068	-41377
chr2	238865144	238865248	E068	-41263
chr2	238874796	238876104	E068	-30407
chr2	238876111	238876550	E068	-29961
chr2	238865051	238865134	E069	-41377
chr2	238865144	238865248	E069	-41263
chr2	238874796	238876104	E069	-30407
chr2	238876111	238876550	E069	-29961
chr2	238864741	238864973	E070	-41538
chr2	238874796	238876104	E070	-30407
chr2	238876111	238876550	E070	-29961
chr2	238874796	238876104	E071	-30407
chr2	238876111	238876550	E071	-29961
chr2	238874796	238876104	E072	-30407
chr2	238876111	238876550	E072	-29961
chr2	238865051	238865134	E073	-41377
chr2	238865144	238865248	E073	-41263
chr2	238874796	238876104	E073	-30407
chr2	238876111	238876550	E073	-29961
chr2	238874796	238876104	E074	-30407
chr2	238876111	238876550	E074	-29961
chr2	238876111	238876550	E081	-29961
chr2	238864688	238864740	E082	-41771
chr2	238864741	238864973	E082	-41538
chr2	238865051	238865134	E082	-41377
chr2	238865144	238865248	E082	-41263
chr2	238874796	238876104	E082	-30407
chr2	238876111	238876550	E082	-29961