rs2252822

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 (3749/29934,GnomAD)
A==0126 (3696/29118,TOPMED)
A==0147 (734/5008,1000G)

Position: chr2:238074626 (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.238074626A>G
GRCh37.p13 chr 2	NC_000002.11:g.238983267A>G

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	G=0.917
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 Genome Aggregation Database	African	Sub	8716	A=0.102	G=0.898
The Genome Aggregation Database	American	Sub	838	A=0.170	G=0.830
The Genome Aggregation Database	East Asian	Sub	1622	A=0.025	G=0.975
The Genome Aggregation Database	Europe	Sub	18456	A=0.143	G=0.856
The Genome Aggregation Database	Global	Study-wide	29934	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=0.126	G=0.873

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
rs2252822	0.000132	alcohol consumption	23743675

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238983267	SCLY	ENSG00000132330.12	A>G	7.8532e-10	13737	Cerebellum
Chr2:238983267	SCLY	ENSG00000132330.12	A>G	2.8719e-4	13737	Frontal_Cortex_BA9
Chr2:238983267	SCLY	ENSG00000132330.12	A>G	1.0714e-8	13737	Cortex
Chr2:238983267	SCLY	ENSG00000132330.12	A>G	2.0850e-8	13737	Cerebellar_Hemisphere
Chr2:238983267	SCLY	ENSG00000132330.12	A>G	1.4177e-3	13737	Caudate_basal_ganglia
Chr2:238983267	SCLY	ENSG00000132330.12	A>G	7.2091e-4	13737	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	-32820
chr2	238951505	238951913	E067	-31354
chr2	238970839	238970899	E067	-12368
chr2	238990205	238990255	E067	6938
chr2	238990452	238990751	E067	7185
chr2	238970839	238970899	E068	-12368
chr2	239017313	239017876	E068	34046
chr2	238951505	238951913	E069	-31354
chr2	238970839	238970899	E069	-12368
chr2	238989790	238989866	E069	6523
chr2	238989941	238990032	E069	6674
chr2	238990205	238990255	E069	6938
chr2	238970839	238970899	E070	-12368
chr2	238950342	238950447	E071	-32820
chr2	238951505	238951913	E071	-31354
chr2	238951961	238952020	E071	-31247
chr2	238970839	238970899	E071	-12368
chr2	238989247	238989354	E071	5980
chr2	238989790	238989866	E071	6523
chr2	238989941	238990032	E071	6674
chr2	238990205	238990255	E071	6938
chr2	238990452	238990751	E071	7185
chr2	239007116	239007529	E071	23849
chr2	239017176	239017226	E071	33909
chr2	239017313	239017876	E071	34046
chr2	238950342	238950447	E072	-32820
chr2	238989790	238989866	E072	6523
chr2	238989941	238990032	E072	6674
chr2	238990205	238990255	E072	6938
chr2	238990452	238990751	E072	7185
chr2	239014417	239014467	E072	31150
chr2	239014951	239015001	E072	31684
chr2	238970839	238970899	E073	-12368
chr2	239014951	239015001	E073	31684
chr2	238950342	238950447	E074	-32820
chr2	238951505	238951913	E074	-31354
chr2	238989790	238989866	E074	6523
chr2	238989941	238990032	E074	6674
chr2	238990452	238990751	E074	7185
chr2	239017313	239017876	E074	34046
chr2	238994008	238994058	E081	10741
chr2	238994372	238994803	E081	11105
chr2	238993565	238993671	E082	10298
chr2	238994008	238994058	E082	10741

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-12660
chr2	238968700	238970607	E068	-12660
chr2	238968700	238970607	E069	-12660
chr2	238968700	238970607	E070	-12660
chr2	238968700	238970607	E071	-12660
chr2	238968700	238970607	E072	-12660
chr2	238968700	238970607	E073	-12660
chr2	238968700	238970607	E074	-12660
chr2	238968700	238970607	E081	-12660
chr2	238968700	238970607	E082	-12660