rs2592585

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0140 (4190/29764,GnomAD)
T=0150 (4379/29118,TOPMED)
T=0164 (819/5008,1000G)
T=0176 (679/3854,ALSPAC)
T=0189 (700/3708,TWINSUK)

Position: chr2:238070980 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 46 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238070980C>T
GRCh37.p13 chr 2	NC_000002.11:g.238979621C>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	C=0.853	T=0.147
1000Genomes	American	Sub	694	C=0.820	T=0.180
1000Genomes	East Asian	Sub	1008	C=0.971	T=0.029
1000Genomes	Europe	Sub	1006	C=0.837	T=0.163
1000Genomes	Global	Study-wide	5008	C=0.836	T=0.164
1000Genomes	South Asian	Sub	978	C=0.690	T=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.824	T=0.176
The Genome Aggregation Database	African	Sub	8666	C=0.845	T=0.155
The Genome Aggregation Database	American	Sub	836	C=0.820	T=0.180
The Genome Aggregation Database	East Asian	Sub	1612	C=0.973	T=0.027
The Genome Aggregation Database	Europe	Sub	18348	C=0.856	T=0.143
The Genome Aggregation Database	Global	Study-wide	29764	C=0.859	T=0.140
The Genome Aggregation Database	Other	Sub	302	C=0.900	T=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.849	T=0.150
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.811	T=0.189

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
rs2592585	9.57E-05	alcohol consumption	23743675

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238979621	SCLY	ENSG00000132330.12	C>T	7.8532e-10	10091	Cerebellum
Chr2:238979621	SCLY	ENSG00000132330.12	C>T	1.0714e-8	10091	Cortex
Chr2:238979621	SCLY	ENSG00000132330.12	C>T	2.0850e-8	10091	Cerebellar_Hemisphere
Chr2:238979621	SCLY	ENSG00000132330.12	C>T	1.4177e-3	10091	Caudate_basal_ganglia
Chr2:238979621	SCLY	ENSG00000132330.12	C>T	2.3006e-3	10091	Substantia_nigra
Chr2:238979621	SCLY	ENSG00000132330.12	C>T	7.2091e-4	10091	Anterior_cingulate_cortex

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0645599800790513	1.4233e-14

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238931681	238931768	E067	-47853
chr2	238950342	238950447	E067	-29174
chr2	238951505	238951913	E067	-27708
chr2	238970839	238970899	E067	-8722
chr2	238990205	238990255	E067	10584
chr2	238990452	238990751	E067	10831
chr2	238970839	238970899	E068	-8722
chr2	239017313	239017876	E068	37692
chr2	238951505	238951913	E069	-27708
chr2	238970839	238970899	E069	-8722
chr2	238989790	238989866	E069	10169
chr2	238989941	238990032	E069	10320
chr2	238990205	238990255	E069	10584
chr2	238970839	238970899	E070	-8722
chr2	238950342	238950447	E071	-29174
chr2	238951505	238951913	E071	-27708
chr2	238951961	238952020	E071	-27601
chr2	238970839	238970899	E071	-8722
chr2	238989247	238989354	E071	9626
chr2	238989790	238989866	E071	10169
chr2	238989941	238990032	E071	10320
chr2	238990205	238990255	E071	10584
chr2	238990452	238990751	E071	10831
chr2	239007116	239007529	E071	27495
chr2	239017176	239017226	E071	37555
chr2	239017313	239017876	E071	37692
chr2	238950342	238950447	E072	-29174
chr2	238989790	238989866	E072	10169
chr2	238989941	238990032	E072	10320
chr2	238990205	238990255	E072	10584
chr2	238990452	238990751	E072	10831
chr2	239014417	239014467	E072	34796
chr2	239014951	239015001	E072	35330
chr2	238970839	238970899	E073	-8722
chr2	239014951	239015001	E073	35330
chr2	238931681	238931768	E074	-47853
chr2	238950342	238950447	E074	-29174
chr2	238951505	238951913	E074	-27708
chr2	238989790	238989866	E074	10169
chr2	238989941	238990032	E074	10320
chr2	238990452	238990751	E074	10831
chr2	239017313	239017876	E074	37692
chr2	238994008	238994058	E081	14387
chr2	238994372	238994803	E081	14751
chr2	238993565	238993671	E082	13944
chr2	238994008	238994058	E082	14387

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-9014
chr2	238968700	238970607	E068	-9014
chr2	238968700	238970607	E069	-9014
chr2	238968700	238970607	E070	-9014
chr2	238968700	238970607	E071	-9014
chr2	238968700	238970607	E072	-9014
chr2	238968700	238970607	E073	-9014
chr2	238968700	238970607	E074	-9014
chr2	238968700	238970607	E081	-9014
chr2	238968700	238970607	E082	-9014