rs821490

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==0138 (4155/29934,GnomAD)
G==0148 (4322/29118,TOPMED)
G==0164 (820/5008,1000G)
G==0177 (681/3854,ALSPAC)
G==0190 (705/3708,TWINSUK)

Position: chr2:238051931 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 56 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.238051931G>A
GRCh37.p13 chr 2	NC_000002.11:g.238960572G>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=0.147	A=0.853
1000Genomes	American	Sub	694	G=0.180	A=0.820
1000Genomes	East Asian	Sub	1008	G=0.029	A=0.971
1000Genomes	Europe	Sub	1006	G=0.165	A=0.835
1000Genomes	Global	Study-wide	5008	G=0.164	A=0.836
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	8718	G=0.146	A=0.854
The Genome Aggregation Database	American	Sub	838	G=0.180	A=0.820
The Genome Aggregation Database	East Asian	Sub	1622	G=0.025	A=0.975
The Genome Aggregation Database	Europe	Sub	18454	G=0.144	A=0.855
The Genome Aggregation Database	Global	Study-wide	29934	G=0.138	A=0.861
The Genome Aggregation Database	Other	Sub	302	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.148	A=0.851
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
rs821490	0.000141	alcohol consumption	23743675

eQTL of rs821490 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238960572	SCLY	ENSG00000132330.12	G>A	7.8532e-10	-8958	Cerebellum
Chr2:238960572	SCLY	ENSG00000132330.12	G>A	1.0714e-8	-8958	Cortex
Chr2:238960572	SCLY	ENSG00000132330.12	G>A	2.0850e-8	-8958	Cerebellar_Hemisphere
Chr2:238960572	SCLY	ENSG00000132330.12	G>A	1.4177e-3	-8958	Caudate_basal_ganglia
Chr2:238960572	SCLY	ENSG00000132330.12	G>A	7.2091e-4	-8958	Anterior_cingulate_cortex

meQTL of rs821490 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	238917607	238917771	E067	-42801
chr2	238931681	238931768	E067	-28804
chr2	238950342	238950447	E067	-10125
chr2	238951505	238951913	E067	-8659
chr2	238970839	238970899	E067	10267
chr2	238990205	238990255	E067	29633
chr2	238990452	238990751	E067	29880
chr2	238970839	238970899	E068	10267
chr2	238918301	238918438	E069	-42134
chr2	238919370	238919610	E069	-40962
chr2	238919757	238919867	E069	-40705
chr2	238928552	238929028	E069	-31544
chr2	238951505	238951913	E069	-8659
chr2	238970839	238970899	E069	10267
chr2	238989790	238989866	E069	29218
chr2	238989941	238990032	E069	29369
chr2	238990205	238990255	E069	29633
chr2	238970839	238970899	E070	10267
chr2	238917607	238917771	E071	-42801
chr2	238917904	238917968	E071	-42604
chr2	238918301	238918438	E071	-42134
chr2	238919370	238919610	E071	-40962
chr2	238919757	238919867	E071	-40705
chr2	238950342	238950447	E071	-10125
chr2	238951505	238951913	E071	-8659
chr2	238951961	238952020	E071	-8552
chr2	238970839	238970899	E071	10267
chr2	238989247	238989354	E071	28675
chr2	238989790	238989866	E071	29218
chr2	238989941	238990032	E071	29369
chr2	238990205	238990255	E071	29633
chr2	238990452	238990751	E071	29880
chr2	239007116	239007529	E071	46544
chr2	238917607	238917771	E072	-42801
chr2	238950342	238950447	E072	-10125
chr2	238989790	238989866	E072	29218
chr2	238989941	238990032	E072	29369
chr2	238990205	238990255	E072	29633
chr2	238990452	238990751	E072	29880
chr2	238970839	238970899	E073	10267
chr2	238915164	238915422	E074	-45150
chr2	238917607	238917771	E074	-42801
chr2	238917904	238917968	E074	-42604
chr2	238918301	238918438	E074	-42134
chr2	238919370	238919610	E074	-40962
chr2	238919757	238919867	E074	-40705
chr2	238931681	238931768	E074	-28804
chr2	238950342	238950447	E074	-10125
chr2	238951505	238951913	E074	-8659
chr2	238989790	238989866	E074	29218
chr2	238989941	238990032	E074	29369
chr2	238990452	238990751	E074	29880
chr2	238994008	238994058	E081	33436
chr2	238994372	238994803	E081	33800
chr2	238993565	238993671	E082	32993
chr2	238994008	238994058	E082	33436

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	8128
chr2	238968700	238970607	E068	8128
chr2	238968700	238970607	E069	8128
chr2	238968700	238970607	E070	8128
chr2	238968700	238970607	E071	8128
chr2	238968700	238970607	E072	8128
chr2	238968700	238970607	E073	8128
chr2	238968700	238970607	E074	8128
chr2	238968700	238970607	E081	8128
chr2	238968700	238970607	E082	8128