rs821485

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0179 (5337/29788,GnomAD)
A==0210 (6138/29118,TOPMED)
A==0205 (1026/5008,1000G)
A==0177 (681/3854,ALSPAC)
A==0189 (702/3708,TWINSUK)

Position: chr2:238058166 (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.238058166A>G
GRCh37.p13 chr 2	NC_000002.11:g.238966807A>G

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	A=0.299	G=0.701
1000Genomes	American	Sub	694	A=0.190	G=0.810
1000Genomes	East Asian	Sub	1008	A=0.029	G=0.971
1000Genomes	Europe	Sub	1006	A=0.163	G=0.837
1000Genomes	Global	Study-wide	5008	A=0.205	G=0.795
1000Genomes	South Asian	Sub	978	A=0.310	G=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.177	G=0.823
The Genome Aggregation Database	African	Sub	8636	A=0.287	G=0.713
The Genome Aggregation Database	American	Sub	830	A=0.180	G=0.820
The Genome Aggregation Database	East Asian	Sub	1620	A=0.025	G=0.975
The Genome Aggregation Database	Europe	Sub	18400	A=0.143	G=0.856
The Genome Aggregation Database	Global	Study-wide	29788	A=0.179	G=0.820
The Genome Aggregation Database	Other	Sub	302	A=0.100	G=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.210	G=0.789
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.189	G=0.811

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
rs821485	6.82E-05	alcohol consumption	23743675

eQTL of rs821485 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238966807	SCLY	ENSG00000132330.12	A>G	7.8532e-10	-2723	Cerebellum
Chr2:238966807	SCLY	ENSG00000132330.12	A>G	1.0714e-8	-2723	Cortex
Chr2:238966807	SCLY	ENSG00000132330.12	A>G	2.0850e-8	-2723	Cerebellar_Hemisphere
Chr2:238966807	SCLY	ENSG00000132330.12	A>G	1.4177e-3	-2723	Caudate_basal_ganglia
Chr2:238966807	SCLY	ENSG00000132330.12	A>G	7.2091e-4	-2723	Anterior_cingulate_cortex

meQTL of rs821485 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	-49036
chr2	238931681	238931768	E067	-35039
chr2	238950342	238950447	E067	-16360
chr2	238951505	238951913	E067	-14894
chr2	238970839	238970899	E067	4032
chr2	238990205	238990255	E067	23398
chr2	238990452	238990751	E067	23645
chr2	238970839	238970899	E068	4032
chr2	238918301	238918438	E069	-48369
chr2	238919370	238919610	E069	-47197
chr2	238919757	238919867	E069	-46940
chr2	238928552	238929028	E069	-37779
chr2	238951505	238951913	E069	-14894
chr2	238970839	238970899	E069	4032
chr2	238989790	238989866	E069	22983
chr2	238989941	238990032	E069	23134
chr2	238990205	238990255	E069	23398
chr2	238970839	238970899	E070	4032
chr2	238917607	238917771	E071	-49036
chr2	238917904	238917968	E071	-48839
chr2	238918301	238918438	E071	-48369
chr2	238919370	238919610	E071	-47197
chr2	238919757	238919867	E071	-46940
chr2	238950342	238950447	E071	-16360
chr2	238951505	238951913	E071	-14894
chr2	238951961	238952020	E071	-14787
chr2	238970839	238970899	E071	4032
chr2	238989247	238989354	E071	22440
chr2	238989790	238989866	E071	22983
chr2	238989941	238990032	E071	23134
chr2	238990205	238990255	E071	23398
chr2	238990452	238990751	E071	23645
chr2	239007116	239007529	E071	40309
chr2	238917607	238917771	E072	-49036
chr2	238950342	238950447	E072	-16360
chr2	238989790	238989866	E072	22983
chr2	238989941	238990032	E072	23134
chr2	238990205	238990255	E072	23398
chr2	238990452	238990751	E072	23645
chr2	239014417	239014467	E072	47610
chr2	239014951	239015001	E072	48144
chr2	238970839	238970899	E073	4032
chr2	239014951	239015001	E073	48144
chr2	238917607	238917771	E074	-49036
chr2	238917904	238917968	E074	-48839
chr2	238918301	238918438	E074	-48369
chr2	238919370	238919610	E074	-47197
chr2	238919757	238919867	E074	-46940
chr2	238931681	238931768	E074	-35039
chr2	238950342	238950447	E074	-16360
chr2	238951505	238951913	E074	-14894
chr2	238989790	238989866	E074	22983
chr2	238989941	238990032	E074	23134
chr2	238990452	238990751	E074	23645
chr2	238994008	238994058	E081	27201
chr2	238994372	238994803	E081	27565
chr2	238993565	238993671	E082	26758
chr2	238994008	238994058	E082	27201

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	1893
chr2	238968700	238970607	E068	1893
chr2	238968700	238970607	E069	1893
chr2	238968700	238970607	E070	1893
chr2	238968700	238970607	E071	1893
chr2	238968700	238970607	E072	1893
chr2	238968700	238970607	E073	1893
chr2	238968700	238970607	E074	1893
chr2	238968700	238970607	E081	1893
chr2	238968700	238970607	E082	1893