rs2250039

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0139 (4157/29890,GnomAD)
G==0148 (4313/29118,TOPMED)
G==0165 (824/5008,1000G)
G==0177 (681/3854,ALSPAC)
G==0189 (701/3708,TWINSUK)

Position: chr2:238062296 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 47 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.238062296G>A
GRCh37.p13 chr 2	NC_000002.11:g.238970937G>A

Gene: SCLY, selenocysteine lyase(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCLY transcript	NM_016510.5:c.	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=0.151	A=0.849
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=0.163	A=0.837
1000Genomes	Global	Study-wide	5008	G=0.165	A=0.835
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	8698	G=0.148	A=0.852
The Genome Aggregation Database	American	Sub	838	G=0.180	A=0.820
The Genome Aggregation Database	East Asian	Sub	1620	G=0.026	A=0.974
The Genome Aggregation Database	Europe	Sub	18436	G=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29890	G=0.139	A=0.860
The Genome Aggregation Database	Other	Sub	298	G=0.100	A=0.900
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=0.189	A=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
rs2250039	6.23E-05	alcohol consumption	23743675

eQTL of rs2250039 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238970937	SCLY	ENSG00000132330.12	G>A	7.8532e-10	1407	Cerebellum
Chr2:238970937	SCLY	ENSG00000132330.12	G>A	1.0714e-8	1407	Cortex
Chr2:238970937	SCLY	ENSG00000132330.12	G>A	2.0850e-8	1407	Cerebellar_Hemisphere
Chr2:238970937	SCLY	ENSG00000132330.12	G>A	1.4177e-3	1407	Caudate_basal_ganglia
Chr2:238970937	SCLY	ENSG00000132330.12	G>A	7.2091e-4	1407	Anterior_cingulate_cortex

meQTL of rs2250039 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	-39169
chr2	238950342	238950447	E067	-20490
chr2	238951505	238951913	E067	-19024
chr2	238970839	238970899	E067	-38
chr2	238990205	238990255	E067	19268
chr2	238990452	238990751	E067	19515
chr2	238970839	238970899	E068	-38
chr2	239017313	239017876	E068	46376
chr2	238928552	238929028	E069	-41909
chr2	238951505	238951913	E069	-19024
chr2	238970839	238970899	E069	-38
chr2	238989790	238989866	E069	18853
chr2	238989941	238990032	E069	19004
chr2	238990205	238990255	E069	19268
chr2	238970839	238970899	E070	-38
chr2	238950342	238950447	E071	-20490
chr2	238951505	238951913	E071	-19024
chr2	238951961	238952020	E071	-18917
chr2	238970839	238970899	E071	-38
chr2	238989247	238989354	E071	18310
chr2	238989790	238989866	E071	18853
chr2	238989941	238990032	E071	19004
chr2	238990205	238990255	E071	19268
chr2	238990452	238990751	E071	19515
chr2	239007116	239007529	E071	36179
chr2	239017176	239017226	E071	46239
chr2	239017313	239017876	E071	46376
chr2	238950342	238950447	E072	-20490
chr2	238989790	238989866	E072	18853
chr2	238989941	238990032	E072	19004
chr2	238990205	238990255	E072	19268
chr2	238990452	238990751	E072	19515
chr2	239014417	239014467	E072	43480
chr2	239014951	239015001	E072	44014
chr2	238970839	238970899	E073	-38
chr2	239014951	239015001	E073	44014
chr2	238931681	238931768	E074	-39169
chr2	238950342	238950447	E074	-20490
chr2	238951505	238951913	E074	-19024
chr2	238989790	238989866	E074	18853
chr2	238989941	238990032	E074	19004
chr2	238990452	238990751	E074	19515
chr2	239017313	239017876	E074	46376
chr2	238994008	238994058	E081	23071
chr2	238994372	238994803	E081	23435
chr2	238993565	238993671	E082	22628
chr2	238994008	238994058	E082	23071

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-330
chr2	238968700	238970607	E068	-330
chr2	238968700	238970607	E069	-330
chr2	238968700	238970607	E070	-330
chr2	238968700	238970607	E071	-330
chr2	238968700	238970607	E072	-330
chr2	238968700	238970607	E073	-330
chr2	238968700	238970607	E074	-330
chr2	238968700	238970607	E081	-330
chr2	238968700	238970607	E082	-330