rs9288318

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

ALS2CR12 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0349 (10446/29876,GnomAD)
C==0352 (10276/29118,TOPMED)
C==0299 (1497/5008,1000G)
C==0383 (1477/3854,ALSPAC)
C==0393 (1458/3708,TWINSUK)

Position: chr2:201331340 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 1 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.201331340C>A
GRCh37.p13 chr 2	NC_000002.11:g.202196063C>A

Gene: ALS2CR12, amyotrophic lateral sclerosis 2 chromosome region candidate 12(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ALS2CR12 transcript variant 2	NM_001127391.2:c.	N/A	Intron Variant
ALS2CR12 transcript variant 3	NM_001289993.1:c.	N/A	Intron Variant
ALS2CR12 transcript variant 1	NM_139163.3:c.	N/A	Intron Variant
ALS2CR12 transcript variant 4	NR_110620.1:n.	N/A	Intron Variant
ALS2CR12 transcript variant X1	XM_011510606.2:c.	N/A	Intron Variant
ALS2CR12 transcript variant X3	XM_011510610.2:c.	N/A	Intron Variant
ALS2CR12 transcript variant X6	XM_011510612.2:c.	N/A	Intron Variant
ALS2CR12 transcript variant X2	XM_017003360.1:c.	N/A	Intron Variant
ALS2CR12 transcript variant X4	XM_017003361.1:c.	N/A	Intron Variant
ALS2CR12 transcript variant X5	XM_017003362.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.222	A=0.778
1000Genomes	American	Sub	694	C=0.510	A=0.490
1000Genomes	East Asian	Sub	1008	C=0.295	A=0.705
1000Genomes	Europe	Sub	1006	C=0.395	A=0.605
1000Genomes	Global	Study-wide	5008	C=0.299	A=0.701
1000Genomes	South Asian	Sub	978	C=0.160	A=0.840
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.383	A=0.617
The Genome Aggregation Database	African	Sub	8702	C=0.264	A=0.736
The Genome Aggregation Database	American	Sub	836	C=0.500	A=0.500
The Genome Aggregation Database	East Asian	Sub	1608	C=0.263	A=0.737
The Genome Aggregation Database	Europe	Sub	18428	C=0.389	A=0.610
The Genome Aggregation Database	Global	Study-wide	29876	C=0.349	A=0.650
The Genome Aggregation Database	Other	Sub	302	C=0.440	A=0.560
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.352	A=0.647
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.393	A=0.607

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
22323360	Genotypic variants at 2q33 and risk of esophageal squamous cell carcinoma in China: a meta-analysis of genome-wide association studies.	Abnet CC	Hum Mol Genet

P-Value

SNP ID	p-value	Traits	Study
rs9288318	0.00064	alcohol dependence	20201924

eQTL of rs9288318 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:202196063	CASP8	ENSG00000064012.17	C>A	1.1692e-16	97897	Cerebellum
Chr2:202196063	CASP8	ENSG00000064012.17	C>A	6.4882e-11	97897	Frontal_Cortex_BA9
Chr2:202196063	CASP8	ENSG00000064012.17	C>A	1.3634e-11	97897	Cortex
Chr2:202196063	ALS2CR12	ENSG00000155749.8	C>A	3.6640e-13	-26058	Cortex
Chr2:202196063	CASP8	ENSG00000064012.17	C>A	3.9218e-19	97897	Cerebellar_Hemisphere
Chr2:202196063	ALS2CR12	ENSG00000155749.8	C>A	3.5575e-7	-26058	Caudate_basal_ganglia

meQTL of rs9288318 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	202227603	202227687	E068	31540