SNP Detail Info-rs62196004

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:

A=0126 (3764/29814,GnomAD)
A=0130 (3801/29118,TOPMED)
A=0148 (741/5008,1000G)
A=0177 (681/3854,ALSPAC)
A=0189 (699/3708,TWINSUK)

Position: chr2:238097673 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 35 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238097673G>A
GRCh37.p13 chr 2	NC_000002.11:g.239006314G>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=0.911	A=0.089
1000Genomes	American	Sub	694	G=0.820	A=0.180
1000Genomes	East Asian	Sub	1008	G=0.971	A=0.029
1000Genomes	Europe	Sub	1006	G=0.838	A=0.162
1000Genomes	Global	Study-wide	5008	G=0.852	A=0.148
1000Genomes	South Asian	Sub	978	G=0.690	A=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.823	A=0.177
The Genome Aggregation Database	African	Sub	8660	G=0.894	A=0.106
The Genome Aggregation Database	American	Sub	838	G=0.820	A=0.180
The Genome Aggregation Database	East Asian	Sub	1620	G=0.975	A=0.025
The Genome Aggregation Database	Europe	Sub	18396	G=0.857	A=0.143
The Genome Aggregation Database	Global	Study-wide	29814	G=0.873	A=0.126
The Genome Aggregation Database	Other	Sub	300	G=0.890	A=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.869	A=0.130
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.811	A=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
rs62196004	0.000107	alcohol consumption	23743675

eQTL of rs62196004 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:239006314	SCLY	ENSG00000132330.12	G>A	7.8532e-10	36784	Cerebellum
Chr2:239006314	SCLY	ENSG00000132330.12	G>A	2.8719e-4	36784	Frontal_Cortex_BA9
Chr2:239006314	SCLY	ENSG00000132330.12	G>A	1.0714e-8	36784	Cortex
Chr2:239006314	SCLY	ENSG00000132330.12	G>A	2.0850e-8	36784	Cerebellar_Hemisphere
Chr2:239006314	SCLY	ENSG00000132330.12	G>A	1.4177e-3	36784	Caudate_basal_ganglia
Chr2:239006314	SCLY	ENSG00000132330.12	G>A	7.2091e-4	36784	Anterior_cingulate_cortex

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0645355740015763	3.5581e-14

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238970839	238970899	E067	-35415
chr2	238990205	238990255	E067	-16059
chr2	238990452	238990751	E067	-15563
chr2	238970839	238970899	E068	-35415
chr2	239017313	239017876	E068	10999
chr2	238970839	238970899	E069	-35415
chr2	238989790	238989866	E069	-16448
chr2	238989941	238990032	E069	-16282
chr2	238990205	238990255	E069	-16059
chr2	238970839	238970899	E070	-35415
chr2	238970839	238970899	E071	-35415
chr2	238989247	238989354	E071	-16960
chr2	238989790	238989866	E071	-16448
chr2	238989941	238990032	E071	-16282
chr2	238990205	238990255	E071	-16059
chr2	238990452	238990751	E071	-15563
chr2	239007116	239007529	E071	802
chr2	239017176	239017226	E071	10862
chr2	239017313	239017876	E071	10999
chr2	238989790	238989866	E072	-16448
chr2	238989941	238990032	E072	-16282
chr2	238990205	238990255	E072	-16059
chr2	238990452	238990751	E072	-15563
chr2	239014417	239014467	E072	8103
chr2	239014951	239015001	E072	8637
chr2	238970839	238970899	E073	-35415
chr2	239014951	239015001	E073	8637
chr2	238989790	238989866	E074	-16448
chr2	238989941	238990032	E074	-16282
chr2	238990452	238990751	E074	-15563
chr2	239017313	239017876	E074	10999
chr2	238994008	238994058	E081	-12256
chr2	238994372	238994803	E081	-11511
chr2	238993565	238993671	E082	-12643
chr2	238994008	238994058	E082	-12256

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-35707
chr2	238968700	238970607	E068	-35707
chr2	238968700	238970607	E069	-35707
chr2	238968700	238970607	E070	-35707
chr2	238968700	238970607	E071	-35707
chr2	238968700	238970607	E072	-35707
chr2	238968700	238970607	E073	-35707
chr2	238968700	238970607	E074	-35707
chr2	238968700	238970607	E081	-35707
chr2	238968700	238970607	E082	-35707

rs62196004