rs2248825

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==0127 (3808/29800,GnomAD)
G==0130 (3806/29118,TOPMED)
G==0149 (744/5008,1000G)
G==0176 (679/3854,ALSPAC)
G==0188 (697/3708,TWINSUK)

Position: chr2:238084404 (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.238084404G>A
GRCh37.p13 chr 2	NC_000002.11:g.238993045G>A

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	G=0.092	A=0.908
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=0.162	A=0.838
1000Genomes	Global	Study-wide	5008	G=0.149	A=0.851
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=0.176	A=0.824
The Genome Aggregation Database	African	Sub	8680	G=0.111	A=0.889
The Genome Aggregation Database	American	Sub	836	G=0.170	A=0.830
The Genome Aggregation Database	East Asian	Sub	1616	G=0.025	A=0.975
The Genome Aggregation Database	Europe	Sub	18368	G=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29800	G=0.127	A=0.872
The Genome Aggregation Database	Other	Sub	300	G=0.100	A=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.130	A=0.869
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.188	A=0.812

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
rs2248825	6.8E-05	alcohol consumption	23743675

eQTL of rs2248825 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238993045	SCLY	ENSG00000132330.12	G>A	7.8532e-10	23515	Cerebellum
Chr2:238993045	SCLY	ENSG00000132330.12	G>A	2.8719e-4	23515	Frontal_Cortex_BA9
Chr2:238993045	SCLY	ENSG00000132330.12	G>A	1.0714e-8	23515	Cortex
Chr2:238993045	SCLY	ENSG00000132330.12	G>A	2.0850e-8	23515	Cerebellar_Hemisphere
Chr2:238993045	SCLY	ENSG00000132330.12	G>A	1.4177e-3	23515	Caudate_basal_ganglia
Chr2:238993045	SCLY	ENSG00000132330.12	G>A	7.2091e-4	23515	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	-42598
chr2	238951505	238951913	E067	-41132
chr2	238970839	238970899	E067	-22146
chr2	238990205	238990255	E067	-2790
chr2	238990452	238990751	E067	-2294
chr2	238970839	238970899	E068	-22146
chr2	239017313	239017876	E068	24268
chr2	238951505	238951913	E069	-41132
chr2	238970839	238970899	E069	-22146
chr2	238989790	238989866	E069	-3179
chr2	238989941	238990032	E069	-3013
chr2	238990205	238990255	E069	-2790
chr2	238970839	238970899	E070	-22146
chr2	238950342	238950447	E071	-42598
chr2	238951505	238951913	E071	-41132
chr2	238951961	238952020	E071	-41025
chr2	238970839	238970899	E071	-22146
chr2	238989247	238989354	E071	-3691
chr2	238989790	238989866	E071	-3179
chr2	238989941	238990032	E071	-3013
chr2	238990205	238990255	E071	-2790
chr2	238990452	238990751	E071	-2294
chr2	239007116	239007529	E071	14071
chr2	239017176	239017226	E071	24131
chr2	239017313	239017876	E071	24268
chr2	238950342	238950447	E072	-42598
chr2	238989790	238989866	E072	-3179
chr2	238989941	238990032	E072	-3013
chr2	238990205	238990255	E072	-2790
chr2	238990452	238990751	E072	-2294
chr2	239014417	239014467	E072	21372
chr2	239014951	239015001	E072	21906
chr2	238970839	238970899	E073	-22146
chr2	239014951	239015001	E073	21906
chr2	238950342	238950447	E074	-42598
chr2	238951505	238951913	E074	-41132
chr2	238989790	238989866	E074	-3179
chr2	238989941	238990032	E074	-3013
chr2	238990452	238990751	E074	-2294
chr2	239017313	239017876	E074	24268
chr2	238994008	238994058	E081	963
chr2	238994372	238994803	E081	1327
chr2	238993565	238993671	E082	520
chr2	238994008	238994058	E082	963

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-22438
chr2	238968700	238970607	E068	-22438
chr2	238968700	238970607	E069	-22438
chr2	238968700	238970607	E070	-22438
chr2	238968700	238970607	E071	-22438
chr2	238968700	238970607	E072	-22438
chr2	238968700	238970607	E073	-22438
chr2	238968700	238970607	E074	-22438
chr2	238968700	238970607	E081	-22438
chr2	238968700	238970607	E082	-22438