rs2249543

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0125 (3770/29974,GnomAD)
A==0127 (3718/29118,TOPMED)
A==0147 (737/5008,1000G)
A==0176 (679/3854,ALSPAC)
A==0189 (701/3708,TWINSUK)

Position: chr2:238066170 (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.238066170A>G
GRCh37.p13 chr 2	NC_000002.11:g.238974811A>G

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	A=0.085	G=0.915
1000Genomes	American	Sub	694	A=0.180	G=0.820
1000Genomes	East Asian	Sub	1008	A=0.029	G=0.971
1000Genomes	Europe	Sub	1006	A=0.162	G=0.838
1000Genomes	Global	Study-wide	5008	A=0.147	G=0.853
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=0.176	G=0.824
The Genome Aggregation Database	African	Sub	8724	A=0.104	G=0.896
The Genome Aggregation Database	American	Sub	838	A=0.170	G=0.830
The Genome Aggregation Database	East Asian	Sub	1620	A=0.025	G=0.975
The Genome Aggregation Database	Europe	Sub	18490	A=0.143	G=0.856
The Genome Aggregation Database	Global	Study-wide	29974	A=0.125	G=0.874
The Genome Aggregation Database	Other	Sub	302	A=0.100	G=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.127	G=0.872
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
rs2249543	6.73E-05	alcohol consumption	23743675

eQTL of rs2249543 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238974811	SCLY	ENSG00000132330.12	A>G	7.8532e-10	5281	Cerebellum
Chr2:238974811	SCLY	ENSG00000132330.12	A>G	2.8719e-4	5281	Frontal_Cortex_BA9
Chr2:238974811	SCLY	ENSG00000132330.12	A>G	1.0714e-8	5281	Cortex
Chr2:238974811	SCLY	ENSG00000132330.12	A>G	2.0850e-8	5281	Cerebellar_Hemisphere
Chr2:238974811	SCLY	ENSG00000132330.12	A>G	1.4177e-3	5281	Caudate_basal_ganglia
Chr2:238974811	SCLY	ENSG00000132330.12	A>G	7.2091e-4	5281	Anterior_cingulate_cortex

meQTL of rs2249543 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0646226347905888	2.4442e-14

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	-43043
chr2	238950342	238950447	E067	-24364
chr2	238951505	238951913	E067	-22898
chr2	238970839	238970899	E067	-3912
chr2	238990205	238990255	E067	15394
chr2	238990452	238990751	E067	15641
chr2	238970839	238970899	E068	-3912
chr2	239017313	239017876	E068	42502
chr2	238928552	238929028	E069	-45783
chr2	238951505	238951913	E069	-22898
chr2	238970839	238970899	E069	-3912
chr2	238989790	238989866	E069	14979
chr2	238989941	238990032	E069	15130
chr2	238990205	238990255	E069	15394
chr2	238970839	238970899	E070	-3912
chr2	238950342	238950447	E071	-24364
chr2	238951505	238951913	E071	-22898
chr2	238951961	238952020	E071	-22791
chr2	238970839	238970899	E071	-3912
chr2	238989247	238989354	E071	14436
chr2	238989790	238989866	E071	14979
chr2	238989941	238990032	E071	15130
chr2	238990205	238990255	E071	15394
chr2	238990452	238990751	E071	15641
chr2	239007116	239007529	E071	32305
chr2	239017176	239017226	E071	42365
chr2	239017313	239017876	E071	42502
chr2	238950342	238950447	E072	-24364
chr2	238989790	238989866	E072	14979
chr2	238989941	238990032	E072	15130
chr2	238990205	238990255	E072	15394
chr2	238990452	238990751	E072	15641
chr2	239014417	239014467	E072	39606
chr2	239014951	239015001	E072	40140
chr2	238970839	238970899	E073	-3912
chr2	239014951	239015001	E073	40140
chr2	238931681	238931768	E074	-43043
chr2	238950342	238950447	E074	-24364
chr2	238951505	238951913	E074	-22898
chr2	238989790	238989866	E074	14979
chr2	238989941	238990032	E074	15130
chr2	238990452	238990751	E074	15641
chr2	239017313	239017876	E074	42502
chr2	238994008	238994058	E081	19197
chr2	238994372	238994803	E081	19561
chr2	238993565	238993671	E082	18754
chr2	238994008	238994058	E082	19197

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-4204
chr2	238968700	238970607	E068	-4204
chr2	238968700	238970607	E069	-4204
chr2	238968700	238970607	E070	-4204
chr2	238968700	238970607	E071	-4204
chr2	238968700	238970607	E072	-4204
chr2	238968700	238970607	E073	-4204
chr2	238968700	238970607	E074	-4204
chr2	238968700	238970607	E081	-4204
chr2	238968700	238970607	E082	-4204