rs821484

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

UBE2F-SCLY : Intron Variant
SCLY : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0146 (4254/29118,TOPMED)
A==0134 (3647/27202,GnomAD)
A==0164 (819/5008,1000G)
A==0176 (679/3854,ALSPAC)
A==0189 (701/3708,TWINSUK)

Position: chr2:238059011 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 55 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.238059011A>T
GRCh37.p13 chr 2	NC_000002.11:g.238967652A>T

Gene: SCLY, selenocysteine lyase(plus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
SCLY transcript	NM_016510.5:c.	N/A	Upstream Transcript 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	A=0.148	T=0.852
1000Genomes	American	Sub	694	A=0.180	T=0.820
1000Genomes	East Asian	Sub	1008	A=0.029	T=0.971
1000Genomes	Europe	Sub	1006	A=0.163	T=0.837
1000Genomes	Global	Study-wide	5008	A=0.164	T=0.836
1000Genomes	South Asian	Sub	978	A=0.310	T=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.176	T=0.824
The Genome Aggregation Database	African	Sub	7976	A=0.142	T=0.858
The Genome Aggregation Database	American	Sub	764	A=0.170	T=0.830
The Genome Aggregation Database	East Asian	Sub	1542	A=0.026	T=0.974
The Genome Aggregation Database	Europe	Sub	16622	A=0.139	T=0.860
The Genome Aggregation Database	Global	Study-wide	27202	A=0.134	T=0.865
The Genome Aggregation Database	Other	Sub	298	A=0.090	T=0.910
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.146	T=0.853
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.189	T=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
rs821484	6.3E-05	alcohol consumption	23743675

eQTL of rs821484 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs821484 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0595313562867304	1.2684e-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	238931681	238931768	E067	-35884
chr2	238950342	238950447	E067	-17205
chr2	238951505	238951913	E067	-15739
chr2	238970839	238970899	E067	3187
chr2	238990205	238990255	E067	22553
chr2	238990452	238990751	E067	22800
chr2	238970839	238970899	E068	3187
chr2	238918301	238918438	E069	-49214
chr2	238919370	238919610	E069	-48042
chr2	238919757	238919867	E069	-47785
chr2	238928552	238929028	E069	-38624
chr2	238951505	238951913	E069	-15739
chr2	238970839	238970899	E069	3187
chr2	238989790	238989866	E069	22138
chr2	238989941	238990032	E069	22289
chr2	238990205	238990255	E069	22553
chr2	238970839	238970899	E070	3187
chr2	238917904	238917968	E071	-49684
chr2	238918301	238918438	E071	-49214
chr2	238919370	238919610	E071	-48042
chr2	238919757	238919867	E071	-47785
chr2	238950342	238950447	E071	-17205
chr2	238951505	238951913	E071	-15739
chr2	238951961	238952020	E071	-15632
chr2	238970839	238970899	E071	3187
chr2	238989247	238989354	E071	21595
chr2	238989790	238989866	E071	22138
chr2	238989941	238990032	E071	22289
chr2	238990205	238990255	E071	22553
chr2	238990452	238990751	E071	22800
chr2	239007116	239007529	E071	39464
chr2	239017176	239017226	E071	49524
chr2	238950342	238950447	E072	-17205
chr2	238989790	238989866	E072	22138
chr2	238989941	238990032	E072	22289
chr2	238990205	238990255	E072	22553
chr2	238990452	238990751	E072	22800
chr2	239014417	239014467	E072	46765
chr2	239014951	239015001	E072	47299
chr2	238970839	238970899	E073	3187
chr2	239014951	239015001	E073	47299
chr2	238917904	238917968	E074	-49684
chr2	238918301	238918438	E074	-49214
chr2	238919370	238919610	E074	-48042
chr2	238919757	238919867	E074	-47785
chr2	238931681	238931768	E074	-35884
chr2	238950342	238950447	E074	-17205
chr2	238951505	238951913	E074	-15739
chr2	238989790	238989866	E074	22138
chr2	238989941	238990032	E074	22289
chr2	238990452	238990751	E074	22800
chr2	238994008	238994058	E081	26356
chr2	238994372	238994803	E081	26720
chr2	238993565	238993671	E082	25913
chr2	238994008	238994058	E082	26356

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	1048
chr2	238968700	238970607	E068	1048
chr2	238968700	238970607	E069	1048
chr2	238968700	238970607	E070	1048
chr2	238968700	238970607	E071	1048
chr2	238968700	238970607	E072	1048
chr2	238968700	238970607	E073	1048
chr2	238968700	238970607	E074	1048
chr2	238968700	238970607	E081	1048
chr2	238968700	238970607	E082	1048