rs843975

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

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

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0137 (4098/29780,GnomAD)
A==0146 (4278/29118,TOPMED)
A==0164 (819/5008,1000G)
A==0176 (679/3854,ALSPAC)
A==0189 (701/3708,TWINSUK)

Position: chr2:238058924 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 59 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.238058924A>C
GRCh37.p13 chr 2	NC_000002.11:g.238967565A>C

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	C=0.852
1000Genomes	American	Sub	694	A=0.180	C=0.820
1000Genomes	East Asian	Sub	1008	A=0.029	C=0.971
1000Genomes	Europe	Sub	1006	A=0.163	C=0.837
1000Genomes	Global	Study-wide	5008	A=0.164	C=0.836
1000Genomes	South Asian	Sub	978	A=0.310	C=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.176	C=0.824
The Genome Aggregation Database	African	Sub	8672	A=0.146	C=0.854
The Genome Aggregation Database	American	Sub	834	A=0.180	C=0.820
The Genome Aggregation Database	East Asian	Sub	1620	A=0.025	C=0.975
The Genome Aggregation Database	Europe	Sub	18352	A=0.142	C=0.857
The Genome Aggregation Database	Global	Study-wide	29780	A=0.137	C=0.862
The Genome Aggregation Database	Other	Sub	302	A=0.100	C=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.146	C=0.853
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.189	C=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
rs843975	6.66E-05	alcohol consumption	23743675

eQTL of rs843975 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238967565	SCLY	ENSG00000132330.12	A>C	7.8532e-10	-1965	Cerebellum
Chr2:238967565	SCLY	ENSG00000132330.12	A>C	1.0714e-8	-1965	Cortex
Chr2:238967565	SCLY	ENSG00000132330.12	A>C	2.0850e-8	-1965	Cerebellar_Hemisphere
Chr2:238967565	SCLY	ENSG00000132330.12	A>C	1.4177e-3	-1965	Caudate_basal_ganglia

meQTL of rs843975 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	-49794
chr2	238931681	238931768	E067	-35797
chr2	238950342	238950447	E067	-17118
chr2	238951505	238951913	E067	-15652
chr2	238970839	238970899	E067	3274
chr2	238990205	238990255	E067	22640
chr2	238990452	238990751	E067	22887
chr2	238970839	238970899	E068	3274
chr2	238918301	238918438	E069	-49127
chr2	238919370	238919610	E069	-47955
chr2	238919757	238919867	E069	-47698
chr2	238928552	238929028	E069	-38537
chr2	238951505	238951913	E069	-15652
chr2	238970839	238970899	E069	3274
chr2	238989790	238989866	E069	22225
chr2	238989941	238990032	E069	22376
chr2	238990205	238990255	E069	22640
chr2	238970839	238970899	E070	3274
chr2	238917607	238917771	E071	-49794
chr2	238917904	238917968	E071	-49597
chr2	238918301	238918438	E071	-49127
chr2	238919370	238919610	E071	-47955
chr2	238919757	238919867	E071	-47698
chr2	238950342	238950447	E071	-17118
chr2	238951505	238951913	E071	-15652
chr2	238951961	238952020	E071	-15545
chr2	238970839	238970899	E071	3274
chr2	238989247	238989354	E071	21682
chr2	238989790	238989866	E071	22225
chr2	238989941	238990032	E071	22376
chr2	238990205	238990255	E071	22640
chr2	238990452	238990751	E071	22887
chr2	239007116	239007529	E071	39551
chr2	239017176	239017226	E071	49611
chr2	238917607	238917771	E072	-49794
chr2	238950342	238950447	E072	-17118
chr2	238989790	238989866	E072	22225
chr2	238989941	238990032	E072	22376
chr2	238990205	238990255	E072	22640
chr2	238990452	238990751	E072	22887
chr2	239014417	239014467	E072	46852
chr2	239014951	239015001	E072	47386
chr2	238970839	238970899	E073	3274
chr2	239014951	239015001	E073	47386
chr2	238917607	238917771	E074	-49794
chr2	238917904	238917968	E074	-49597
chr2	238918301	238918438	E074	-49127
chr2	238919370	238919610	E074	-47955
chr2	238919757	238919867	E074	-47698
chr2	238931681	238931768	E074	-35797
chr2	238950342	238950447	E074	-17118
chr2	238951505	238951913	E074	-15652
chr2	238989790	238989866	E074	22225
chr2	238989941	238990032	E074	22376
chr2	238990452	238990751	E074	22887
chr2	238994008	238994058	E081	26443
chr2	238994372	238994803	E081	26807
chr2	238993565	238993671	E082	26000
chr2	238994008	238994058	E082	26443

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	1135
chr2	238968700	238970607	E068	1135
chr2	238968700	238970607	E069	1135
chr2	238968700	238970607	E070	1135
chr2	238968700	238970607	E071	1135
chr2	238968700	238970607	E072	1135
chr2	238968700	238970607	E073	1135
chr2	238968700	238970607	E074	1135
chr2	238968700	238970607	E081	1135
chr2	238968700	238970607	E082	1135