rs2264165

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0180 (5399/29842,GnomAD)
G==0212 (6189/29118,TOPMED)
G==0205 (1028/5008,1000G)
G==0177 (682/3854,ALSPAC)
G==0190 (703/3708,TWINSUK)

Position: chr2:238057407 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 58 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238057407G>A
GRCh37.p13 chr 2	NC_000002.11:g.238966048G>A

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=0.298	A=0.702
1000Genomes	American	Sub	694	G=0.190	A=0.810
1000Genomes	East Asian	Sub	1008	G=0.029	A=0.971
1000Genomes	Europe	Sub	1006	G=0.166	A=0.834
1000Genomes	Global	Study-wide	5008	G=0.205	A=0.795
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	8666	G=0.288	A=0.712
The Genome Aggregation Database	American	Sub	834	G=0.180	A=0.820
The Genome Aggregation Database	East Asian	Sub	1616	G=0.026	A=0.974
The Genome Aggregation Database	Europe	Sub	18424	G=0.145	A=0.855
The Genome Aggregation Database	Global	Study-wide	29842	G=0.180	A=0.819
The Genome Aggregation Database	Other	Sub	302	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.212	A=0.787
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
rs2264165	6.66E-05	alcohol consumption	23743675

eQTL of rs2264165 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238966048	SCLY	ENSG00000132330.12	G>A	7.8532e-10	-3482	Cerebellum
Chr2:238966048	SCLY	ENSG00000132330.12	G>A	1.0714e-8	-3482	Cortex
Chr2:238966048	SCLY	ENSG00000132330.12	G>A	2.0850e-8	-3482	Cerebellar_Hemisphere
Chr2:238966048	SCLY	ENSG00000132330.12	G>A	1.4177e-3	-3482	Caudate_basal_ganglia
Chr2:238966048	SCLY	ENSG00000132330.12	G>A	7.2091e-4	-3482	Anterior_cingulate_cortex

meQTL of rs2264165 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0552867947809675	7.5821e-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	238917607	238917771	E067	-48277
chr2	238931681	238931768	E067	-34280
chr2	238950342	238950447	E067	-15601
chr2	238951505	238951913	E067	-14135
chr2	238970839	238970899	E067	4791
chr2	238990205	238990255	E067	24157
chr2	238990452	238990751	E067	24404
chr2	238970839	238970899	E068	4791
chr2	238918301	238918438	E069	-47610
chr2	238919370	238919610	E069	-46438
chr2	238919757	238919867	E069	-46181
chr2	238928552	238929028	E069	-37020
chr2	238951505	238951913	E069	-14135
chr2	238970839	238970899	E069	4791
chr2	238989790	238989866	E069	23742
chr2	238989941	238990032	E069	23893
chr2	238990205	238990255	E069	24157
chr2	238970839	238970899	E070	4791
chr2	238917607	238917771	E071	-48277
chr2	238917904	238917968	E071	-48080
chr2	238918301	238918438	E071	-47610
chr2	238919370	238919610	E071	-46438
chr2	238919757	238919867	E071	-46181
chr2	238950342	238950447	E071	-15601
chr2	238951505	238951913	E071	-14135
chr2	238951961	238952020	E071	-14028
chr2	238970839	238970899	E071	4791
chr2	238989247	238989354	E071	23199
chr2	238989790	238989866	E071	23742
chr2	238989941	238990032	E071	23893
chr2	238990205	238990255	E071	24157
chr2	238990452	238990751	E071	24404
chr2	239007116	239007529	E071	41068
chr2	238917607	238917771	E072	-48277
chr2	238950342	238950447	E072	-15601
chr2	238989790	238989866	E072	23742
chr2	238989941	238990032	E072	23893
chr2	238990205	238990255	E072	24157
chr2	238990452	238990751	E072	24404
chr2	239014417	239014467	E072	48369
chr2	239014951	239015001	E072	48903
chr2	238970839	238970899	E073	4791
chr2	239014951	239015001	E073	48903
chr2	238917607	238917771	E074	-48277
chr2	238917904	238917968	E074	-48080
chr2	238918301	238918438	E074	-47610
chr2	238919370	238919610	E074	-46438
chr2	238919757	238919867	E074	-46181
chr2	238931681	238931768	E074	-34280
chr2	238950342	238950447	E074	-15601
chr2	238951505	238951913	E074	-14135
chr2	238989790	238989866	E074	23742
chr2	238989941	238990032	E074	23893
chr2	238990452	238990751	E074	24404
chr2	238994008	238994058	E081	27960
chr2	238994372	238994803	E081	28324
chr2	238993565	238993671	E082	27517
chr2	238994008	238994058	E082	27960

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	2652
chr2	238968700	238970607	E068	2652
chr2	238968700	238970607	E069	2652
chr2	238968700	238970607	E070	2652
chr2	238968700	238970607	E071	2652
chr2	238968700	238970607	E072	2652
chr2	238968700	238970607	E073	2652
chr2	238968700	238970607	E074	2652
chr2	238968700	238970607	E081	2652
chr2	238968700	238970607	E082	2652