rs2592583

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0131 (3828/29118,TOPMED)
G==0128 (3693/28846,GnomAD)
G==0149 (747/5008,1000G)
G==0176 (680/3854,ALSPAC)
G==0189 (699/3708,TWINSUK)

Position: chr2:238087119 (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.238087119G>T
GRCh37.p13 chr 2	NC_000002.11:g.238995760G>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	G=0.094	T=0.906
1000Genomes	American	Sub	694	G=0.180	T=0.820
1000Genomes	East Asian	Sub	1008	G=0.029	T=0.971
1000Genomes	Europe	Sub	1006	G=0.162	T=0.838
1000Genomes	Global	Study-wide	5008	G=0.149	T=0.851
1000Genomes	South Asian	Sub	978	G=0.310	T=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.176	T=0.824
The Genome Aggregation Database	African	Sub	8476	G=0.112	T=0.888
The Genome Aggregation Database	American	Sub	816	G=0.170	T=0.830
The Genome Aggregation Database	East Asian	Sub	1614	G=0.025	T=0.975
The Genome Aggregation Database	Europe	Sub	17638	G=0.143	T=0.856
The Genome Aggregation Database	Global	Study-wide	28846	G=0.128	T=0.872
The Genome Aggregation Database	Other	Sub	302	G=0.100	T=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.131	T=0.868
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=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
rs2592583	0.000143	alcohol consumption	23743675

eQTL of rs2592583 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238995760	SCLY	ENSG00000132330.12	G>T	7.8532e-10	26230	Cerebellum
Chr2:238995760	SCLY	ENSG00000132330.12	G>T	2.8719e-4	26230	Frontal_Cortex_BA9
Chr2:238995760	SCLY	ENSG00000132330.12	G>T	1.0714e-8	26230	Cortex
Chr2:238995760	SCLY	ENSG00000132330.12	G>T	2.0850e-8	26230	Cerebellar_Hemisphere
Chr2:238995760	SCLY	ENSG00000132330.12	G>T	1.4177e-3	26230	Caudate_basal_ganglia
Chr2:238995760	SCLY	ENSG00000132330.12	G>T	7.2091e-4	26230	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	-45313
chr2	238951505	238951913	E067	-43847
chr2	238970839	238970899	E067	-24861
chr2	238990205	238990255	E067	-5505
chr2	238990452	238990751	E067	-5009
chr2	238970839	238970899	E068	-24861
chr2	239017313	239017876	E068	21553
chr2	238951505	238951913	E069	-43847
chr2	238970839	238970899	E069	-24861
chr2	238989790	238989866	E069	-5894
chr2	238989941	238990032	E069	-5728
chr2	238990205	238990255	E069	-5505
chr2	238970839	238970899	E070	-24861
chr2	238950342	238950447	E071	-45313
chr2	238951505	238951913	E071	-43847
chr2	238951961	238952020	E071	-43740
chr2	238970839	238970899	E071	-24861
chr2	238989247	238989354	E071	-6406
chr2	238989790	238989866	E071	-5894
chr2	238989941	238990032	E071	-5728
chr2	238990205	238990255	E071	-5505
chr2	238990452	238990751	E071	-5009
chr2	239007116	239007529	E071	11356
chr2	239017176	239017226	E071	21416
chr2	239017313	239017876	E071	21553
chr2	238950342	238950447	E072	-45313
chr2	238989790	238989866	E072	-5894
chr2	238989941	238990032	E072	-5728
chr2	238990205	238990255	E072	-5505
chr2	238990452	238990751	E072	-5009
chr2	239014417	239014467	E072	18657
chr2	239014951	239015001	E072	19191
chr2	238970839	238970899	E073	-24861
chr2	239014951	239015001	E073	19191
chr2	238950342	238950447	E074	-45313
chr2	238951505	238951913	E074	-43847
chr2	238989790	238989866	E074	-5894
chr2	238989941	238990032	E074	-5728
chr2	238990452	238990751	E074	-5009
chr2	239017313	239017876	E074	21553
chr2	238994008	238994058	E081	-1702
chr2	238994372	238994803	E081	-957
chr2	238993565	238993671	E082	-2089
chr2	238994008	238994058	E082	-1702

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-25153
chr2	238968700	238970607	E068	-25153
chr2	238968700	238970607	E069	-25153
chr2	238968700	238970607	E070	-25153
chr2	238968700	238970607	E071	-25153
chr2	238968700	238970607	E072	-25153
chr2	238968700	238970607	E073	-25153
chr2	238968700	238970607	E074	-25153
chr2	238968700	238970607	E081	-25153
chr2	238968700	238970607	E082	-25153