rs10469607

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==0151 (4532/29966,GnomAD)
G==0168 (4917/29118,TOPMED)
G==0178 (893/5008,1000G)
G==0177 (682/3854,ALSPAC)
G==0190 (705/3708,TWINSUK)

Position: chr2:237996150 (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.237996150G>A
GRCh37.p13 chr 2	NC_000002.11:g.238904792G>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=0.198	A=0.802
1000Genomes	American	Sub	694	G=0.180	A=0.820
1000Genomes	East Asian	Sub	1008	G=0.030	A=0.970
1000Genomes	Europe	Sub	1006	G=0.164	A=0.836
1000Genomes	Global	Study-wide	5008	G=0.178	A=0.822
1000Genomes	South Asian	Sub	978	G=0.310	A=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.177	A=0.823
The Genome Aggregation Database	African	Sub	8722	G=0.189	A=0.811
The Genome Aggregation Database	American	Sub	838	G=0.180	A=0.820
The Genome Aggregation Database	East Asian	Sub	1622	G=0.030	A=0.970
The Genome Aggregation Database	Europe	Sub	18482	G=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29966	G=0.151	A=0.848
The Genome Aggregation Database	Other	Sub	302	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.168	A=0.831
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.190	A=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
rs10469607	0.000149	alcohol consumption	23743675

eQTL of rs10469607 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238904792	SCLY	ENSG00000132330.12	G>A	7.8532e-10	-64738	Cerebellum
Chr2:238904792	SCLY	ENSG00000132330.12	G>A	1.0714e-8	-64738	Cortex
Chr2:238904792	SCLY	ENSG00000132330.12	G>A	2.0850e-8	-64738	Cerebellar_Hemisphere
Chr2:238904792	SCLY	ENSG00000132330.12	G>A	1.4177e-3	-64738	Caudate_basal_ganglia
Chr2:238904792	SCLY	ENSG00000132330.12	G>A	2.3006e-3	-64738	Substantia_nigra
Chr2:238904792	SCLY	ENSG00000132330.12	G>A	7.2091e-4	-64738	Anterior_cingulate_cortex

meQTL of rs10469607 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0579651341209116	5.6486e-12

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	-26754
chr2	238878398	238878539	E067	-26253
chr2	238878551	238878601	E067	-26191
chr2	238878666	238878738	E067	-26054
chr2	238879158	238879263	E067	-25529
chr2	238886584	238886634	E067	-18158
chr2	238886907	238887414	E067	-17378
chr2	238888018	238888228	E067	-16564
chr2	238888415	238888465	E067	-16327
chr2	238888921	238888998	E067	-15794
chr2	238889558	238889737	E067	-15055
chr2	238889976	238890179	E067	-14613
chr2	238893121	238893238	E067	-11554
chr2	238904560	238904874	E067	0
chr2	238904955	238905113	E067	163
chr2	238917607	238917771	E067	12815
chr2	238931681	238931768	E067	26889
chr2	238950342	238950447	E067	45550
chr2	238951505	238951913	E067	46713
chr2	238877816	238878038	E068	-26754
chr2	238878398	238878539	E068	-26253
chr2	238878551	238878601	E068	-26191
chr2	238878666	238878738	E068	-26054
chr2	238879158	238879263	E068	-25529
chr2	238886584	238886634	E068	-18158
chr2	238886907	238887414	E068	-17378
chr2	238888018	238888228	E068	-16564
chr2	238888415	238888465	E068	-16327
chr2	238888921	238888998	E068	-15794
chr2	238889558	238889737	E068	-15055
chr2	238889976	238890179	E068	-14613
chr2	238892164	238892276	E068	-12516
chr2	238893121	238893238	E068	-11554
chr2	238877816	238878038	E069	-26754
chr2	238878398	238878539	E069	-26253
chr2	238878551	238878601	E069	-26191
chr2	238878666	238878738	E069	-26054
chr2	238886584	238886634	E069	-18158
chr2	238886907	238887414	E069	-17378
chr2	238888018	238888228	E069	-16564
chr2	238888921	238888998	E069	-15794
chr2	238889558	238889737	E069	-15055
chr2	238893121	238893238	E069	-11554
chr2	238904955	238905113	E069	163
chr2	238918301	238918438	E069	13509
chr2	238919370	238919610	E069	14578
chr2	238919757	238919867	E069	14965
chr2	238928552	238929028	E069	23760
chr2	238951505	238951913	E069	46713
chr2	238886584	238886634	E070	-18158
chr2	238886907	238887414	E070	-17378
chr2	238888921	238888998	E070	-15794
chr2	238878666	238878738	E071	-26054
chr2	238879158	238879263	E071	-25529
chr2	238886011	238886062	E071	-18730
chr2	238886584	238886634	E071	-18158
chr2	238886907	238887414	E071	-17378
chr2	238888018	238888228	E071	-16564
chr2	238888415	238888465	E071	-16327
chr2	238888921	238888998	E071	-15794
chr2	238893121	238893238	E071	-11554
chr2	238917607	238917771	E071	12815
chr2	238917904	238917968	E071	13112
chr2	238918301	238918438	E071	13509
chr2	238919370	238919610	E071	14578
chr2	238919757	238919867	E071	14965
chr2	238950342	238950447	E071	45550
chr2	238951505	238951913	E071	46713
chr2	238951961	238952020	E071	47169
chr2	238867147	238867197	E072	-37595
chr2	238878551	238878601	E072	-26191
chr2	238886011	238886062	E072	-18730
chr2	238886584	238886634	E072	-18158
chr2	238886907	238887414	E072	-17378
chr2	238888018	238888228	E072	-16564
chr2	238888415	238888465	E072	-16327
chr2	238888921	238888998	E072	-15794
chr2	238889558	238889737	E072	-15055
chr2	238893121	238893238	E072	-11554
chr2	238917607	238917771	E072	12815
chr2	238950342	238950447	E072	45550
chr2	238878551	238878601	E073	-26191
chr2	238878666	238878738	E073	-26054
chr2	238886011	238886062	E073	-18730
chr2	238886584	238886634	E073	-18158
chr2	238886907	238887414	E073	-17378
chr2	238888018	238888228	E073	-16564
chr2	238888415	238888465	E073	-16327
chr2	238888921	238888998	E073	-15794
chr2	238889558	238889737	E073	-15055
chr2	238892164	238892276	E073	-12516
chr2	238893121	238893238	E073	-11554
chr2	238878551	238878601	E074	-26191
chr2	238878666	238878738	E074	-26054
chr2	238879158	238879263	E074	-25529
chr2	238880434	238880549	E074	-24243
chr2	238880894	238880969	E074	-23823
chr2	238884641	238884818	E074	-19974
chr2	238886011	238886062	E074	-18730
chr2	238886584	238886634	E074	-18158
chr2	238886907	238887414	E074	-17378
chr2	238888921	238888998	E074	-15794
chr2	238889558	238889737	E074	-15055
chr2	238889976	238890179	E074	-14613
chr2	238893121	238893238	E074	-11554
chr2	238904560	238904874	E074	0
chr2	238904955	238905113	E074	163
chr2	238915164	238915422	E074	10372
chr2	238917607	238917771	E074	12815
chr2	238917904	238917968	E074	13112
chr2	238918301	238918438	E074	13509
chr2	238919370	238919610	E074	14578
chr2	238919757	238919867	E074	14965
chr2	238931681	238931768	E074	26889
chr2	238950342	238950447	E074	45550
chr2	238951505	238951913	E074	46713
chr2	238877816	238878038	E081	-26754
chr2	238878398	238878539	E081	-26253
chr2	238886907	238887414	E082	-17378

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-28688
chr2	238876111	238876550	E067	-28242
chr2	238864688	238864740	E068	-40052
chr2	238864741	238864973	E068	-39819
chr2	238865051	238865134	E068	-39658
chr2	238865144	238865248	E068	-39544
chr2	238874796	238876104	E068	-28688
chr2	238876111	238876550	E068	-28242
chr2	238865051	238865134	E069	-39658
chr2	238865144	238865248	E069	-39544
chr2	238874796	238876104	E069	-28688
chr2	238876111	238876550	E069	-28242
chr2	238864741	238864973	E070	-39819
chr2	238874796	238876104	E070	-28688
chr2	238876111	238876550	E070	-28242
chr2	238874796	238876104	E071	-28688
chr2	238876111	238876550	E071	-28242
chr2	238874796	238876104	E072	-28688
chr2	238876111	238876550	E072	-28242
chr2	238865051	238865134	E073	-39658
chr2	238865144	238865248	E073	-39544
chr2	238874796	238876104	E073	-28688
chr2	238876111	238876550	E073	-28242
chr2	238874796	238876104	E074	-28688
chr2	238876111	238876550	E074	-28242
chr2	238876111	238876550	E081	-28242
chr2	238864688	238864740	E082	-40052
chr2	238864741	238864973	E082	-39819
chr2	238865051	238865134	E082	-39658
chr2	238865144	238865248	E082	-39544
chr2	238874796	238876104	E082	-28688
chr2	238876111	238876550	E082	-28242