rs4590982

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CASC18 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0208 (6242/29928,GnomAD)
A=0204 (5940/29118,TOPMED)
A=0189 (948/5008,1000G)
A=0251 (967/3854,ALSPAC)
A=0263 (975/3708,TWINSUK)

Position: chr12:105711045 (GRCh38.p7) (12q23.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 122 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.105711045G>A
GRCh37.p13 chr 12	NC_000012.11:g.106104823G>A

Gene: CASC18, cancer susceptibility candidate 18 (non-protein coding)(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CASC18 transcript variant 2	NR_110108.1:n.	N/A	Intron Variant
CASC18 transcript variant 1	NR_110109.1:n.	N/A	Intron Variant
CASC18 transcript variant 3	NR_110110.1:n.	N/A	Intron Variant
CASC18 transcript variant 4	NR_110111.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.922	A=0.078
1000Genomes	American	Sub	694	G=0.740	A=0.260
1000Genomes	East Asian	Sub	1008	G=0.732	A=0.268
1000Genomes	Europe	Sub	1006	G=0.731	A=0.269
1000Genomes	Global	Study-wide	5008	G=0.811	A=0.189
1000Genomes	South Asian	Sub	978	G=0.870	A=0.130
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.749	A=0.251
The Genome Aggregation Database	African	Sub	8714	G=0.899	A=0.101
The Genome Aggregation Database	American	Sub	838	G=0.710	A=0.290
The Genome Aggregation Database	East Asian	Sub	1608	G=0.716	A=0.284
The Genome Aggregation Database	Europe	Sub	18470	G=0.752	A=0.247
The Genome Aggregation Database	Global	Study-wide	29928	G=0.791	A=0.208
The Genome Aggregation Database	Other	Sub	298	G=0.710	A=0.290
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.796	A=0.204
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.737	A=0.263

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs4590982	4.24E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs4590982 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs4590982 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 )
chr12	106098984	106099040	E067	-5783
chr12	106099523	106099920	E067	-4903
chr12	106099978	106100359	E067	-4464
chr12	106132669	106132747	E067	27846
chr12	106133097	106133163	E067	28274
chr12	106133212	106133282	E067	28389
chr12	106133378	106133506	E067	28555
chr12	106133542	106133647	E067	28719
chr12	106133954	106134022	E067	29131
chr12	106134030	106134527	E067	29207
chr12	106134545	106135299	E067	29722
chr12	106135328	106136648	E067	30505
chr12	106142484	106143403	E067	37661
chr12	106099523	106099920	E068	-4903
chr12	106099978	106100359	E068	-4464
chr12	106118358	106118850	E068	13535
chr12	106118884	106119306	E068	14061
chr12	106132531	106132591	E068	27708
chr12	106133378	106133506	E068	28555
chr12	106133542	106133647	E068	28719
chr12	106133954	106134022	E068	29131
chr12	106134030	106134527	E068	29207
chr12	106134545	106135299	E068	29722
chr12	106098984	106099040	E069	-5783
chr12	106099167	106099330	E069	-5493
chr12	106099344	106099496	E069	-5327
chr12	106099523	106099920	E069	-4903
chr12	106099978	106100359	E069	-4464
chr12	106118358	106118850	E069	13535
chr12	106132531	106132591	E069	27708
chr12	106133954	106134022	E069	29131
chr12	106134030	106134527	E069	29207
chr12	106134545	106135299	E069	29722
chr12	106135328	106136648	E069	30505
chr12	106142484	106143403	E069	37661
chr12	106107525	106107783	E070	2702
chr12	106107813	106107975	E070	2990
chr12	106117031	106117082	E070	12208
chr12	106118358	106118850	E070	13535
chr12	106133542	106133647	E070	28719
chr12	106133954	106134022	E070	29131
chr12	106134030	106134527	E070	29207
chr12	106134545	106135299	E070	29722
chr12	106135328	106136648	E070	30505
chr12	106099344	106099496	E071	-5327
chr12	106099523	106099920	E071	-4903
chr12	106099978	106100359	E071	-4464
chr12	106107525	106107783	E071	2702
chr12	106107813	106107975	E071	2990
chr12	106117116	106117207	E071	12293
chr12	106117301	106117475	E071	12478
chr12	106117563	106117613	E071	12740
chr12	106117742	106117912	E071	12919
chr12	106117913	106117963	E071	13090
chr12	106118358	106118850	E071	13535
chr12	106133954	106134022	E071	29131
chr12	106134030	106134527	E071	29207
chr12	106134545	106135299	E071	29722
chr12	106135328	106136648	E071	30505
chr12	106142484	106143403	E071	37661
chr12	106133212	106133282	E072	28389
chr12	106133378	106133506	E072	28555
chr12	106134030	106134527	E072	29207
chr12	106134545	106135299	E072	29722
chr12	106135328	106136648	E072	30505
chr12	106099978	106100359	E073	-4464
chr12	106132531	106132591	E073	27708
chr12	106134030	106134527	E073	29207
chr12	106134545	106135299	E073	29722
chr12	106135328	106136648	E073	30505
chr12	106142484	106143403	E073	37661
chr12	106099523	106099920	E074	-4903
chr12	106099978	106100359	E074	-4464
chr12	106107525	106107783	E074	2702
chr12	106107813	106107975	E074	2990
chr12	106134545	106135299	E074	29722
chr12	106135328	106136648	E074	30505
chr12	106099523	106099920	E081	-4903
chr12	106099978	106100359	E081	-4464
chr12	106100399	106100960	E081	-3863
chr12	106117116	106117207	E081	12293
chr12	106117301	106117475	E081	12478
chr12	106117563	106117613	E081	12740
chr12	106117742	106117912	E081	12919
chr12	106117913	106117963	E081	13090
chr12	106131786	106132226	E081	26963
chr12	106132285	106132522	E081	27462
chr12	106132531	106132591	E081	27708
chr12	106132669	106132747	E081	27846
chr12	106133097	106133163	E081	28274
chr12	106133212	106133282	E081	28389
chr12	106133378	106133506	E081	28555
chr12	106133542	106133647	E081	28719
chr12	106133954	106134022	E081	29131
chr12	106134030	106134527	E081	29207
chr12	106134545	106135299	E081	29722
chr12	106135328	106136648	E081	30505
chr12	106137100	106137226	E081	32277
chr12	106137352	106137438	E081	32529
chr12	106137447	106137795	E081	32624
chr12	106138241	106138473	E081	33418
chr12	106142484	106143403	E081	37661
chr12	106143939	106143998	E081	39116
chr12	106114756	106115044	E082	9933
chr12	106115094	106115554	E082	10271
chr12	106116389	106116439	E082	11566
chr12	106116536	106116641	E082	11713
chr12	106116674	106116781	E082	11851
chr12	106117742	106117912	E082	12919
chr12	106117913	106117963	E082	13090
chr12	106118358	106118850	E082	13535
chr12	106120584	106120638	E082	15761
chr12	106133097	106133163	E082	28274
chr12	106133212	106133282	E082	28389
chr12	106133378	106133506	E082	28555
chr12	106133542	106133647	E082	28719
chr12	106133954	106134022	E082	29131
chr12	106134030	106134527	E082	29207
chr12	106134545	106135299	E082	29722
chr12	106135328	106136648	E082	30505
chr12	106137100	106137226	E082	32277
chr12	106142484	106143403	E082	37661