rs4663836

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0125 (3750/29964,GnomAD)
A==0126 (3694/29118,TOPMED)
A==0147 (734/5008,1000G)
A==0176 (679/3854,ALSPAC)
A==0189 (699/3708,TWINSUK)

Position: chr2:238078544 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 44 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238078544A>T
GRCh37.p13 chr 2	NC_000002.11:g.238987185A>T

Molecule type	Change	Amino acid[Codon]	SO Term
SCLY transcript	NM_016510.5:c.	N/A	Intron Variant

Molecule type	Change	Amino acid[Codon]	SO Term
UBE2F-SCLY transcript	NR_037904.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.083	T=0.917
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=0.162	T=0.838
1000Genomes	Global	Study-wide	5008	A=0.147	T=0.853
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	8726	A=0.102	T=0.898
The Genome Aggregation Database	American	Sub	838	A=0.170	T=0.830
The Genome Aggregation Database	East Asian	Sub	1622	A=0.025	T=0.975
The Genome Aggregation Database	Europe	Sub	18476	A=0.143	T=0.856
The Genome Aggregation Database	Global	Study-wide	29964	A=0.125	T=0.874
The Genome Aggregation Database	Other	Sub	302	A=0.100	T=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.126	T=0.873
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

SNP ID	p-value	Traits	Study
rs4663836	9.6E-05	alcohol consumption	23743675

eQTL of rs4663836 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238987185	SCLY	ENSG00000132330.12	A>T	7.8532e-10	17655	Cerebellum
Chr2:238987185	SCLY	ENSG00000132330.12	A>T	2.8719e-4	17655	Frontal_Cortex_BA9
Chr2:238987185	SCLY	ENSG00000132330.12	A>T	1.0714e-8	17655	Cortex
Chr2:238987185	SCLY	ENSG00000132330.12	A>T	2.0850e-8	17655	Cerebellar_Hemisphere
Chr2:238987185	SCLY	ENSG00000132330.12	A>T	7.2091e-4	17655	Anterior_cingulate_cortex

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

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238950342	238950447	E067	-36738
chr2	238951505	238951913	E067	-35272
chr2	238970839	238970899	E067	-16286
chr2	238990205	238990255	E067	3020
chr2	238990452	238990751	E067	3267
chr2	238970839	238970899	E068	-16286
chr2	239017313	239017876	E068	30128
chr2	238951505	238951913	E069	-35272
chr2	238970839	238970899	E069	-16286
chr2	238989790	238989866	E069	2605
chr2	238989941	238990032	E069	2756
chr2	238990205	238990255	E069	3020
chr2	238970839	238970899	E070	-16286
chr2	238950342	238950447	E071	-36738
chr2	238951505	238951913	E071	-35272
chr2	238951961	238952020	E071	-35165
chr2	238970839	238970899	E071	-16286
chr2	238989247	238989354	E071	2062
chr2	238989790	238989866	E071	2605
chr2	238989941	238990032	E071	2756
chr2	238990205	238990255	E071	3020
chr2	238990452	238990751	E071	3267
chr2	239007116	239007529	E071	19931
chr2	239017176	239017226	E071	29991
chr2	239017313	239017876	E071	30128
chr2	238950342	238950447	E072	-36738
chr2	238989790	238989866	E072	2605
chr2	238989941	238990032	E072	2756
chr2	238990205	238990255	E072	3020
chr2	238990452	238990751	E072	3267
chr2	239014417	239014467	E072	27232
chr2	239014951	239015001	E072	27766
chr2	238970839	238970899	E073	-16286
chr2	239014951	239015001	E073	27766
chr2	238950342	238950447	E074	-36738
chr2	238951505	238951913	E074	-35272
chr2	238989790	238989866	E074	2605
chr2	238989941	238990032	E074	2756
chr2	238990452	238990751	E074	3267
chr2	239017313	239017876	E074	30128
chr2	238994008	238994058	E081	6823
chr2	238994372	238994803	E081	7187
chr2	238993565	238993671	E082	6380
chr2	238994008	238994058	E082	6823

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-16578
chr2	238968700	238970607	E068	-16578
chr2	238968700	238970607	E069	-16578
chr2	238968700	238970607	E070	-16578
chr2	238968700	238970607	E071	-16578
chr2	238968700	238970607	E072	-16578
chr2	238968700	238970607	E073	-16578
chr2	238968700	238970607	E074	-16578
chr2	238968700	238970607	E081	-16578
chr2	238968700	238970607	E082	-16578