rs531454

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CDCA8 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0465 (13930/29924,GnomAD)
A==0442 (12888/29118,TOPMED)
A==0418 (2093/5008,1000G)
G=0424 (1636/3854,ALSPAC)
G=0438 (1623/3708,TWINSUK)

Position: chr1:37707925 (GRCh38.p7) (1p34.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 48 Enhancers around

Promoter: 49 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.37707925A>G
GRCh37.p13 chr 1	NC_000001.10:g.38173597A>G

Molecule type	Change	Amino acid[Codon]	SO Term
CDCA8 transcript variant 1	NM_001256875.1:c.	N/A	Intron Variant
CDCA8 transcript variant 2	NM_018101.3:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.313	G=0.687
1000Genomes	American	Sub	694	A=0.470	G=0.530
1000Genomes	East Asian	Sub	1008	A=0.298	G=0.702
1000Genomes	Europe	Sub	1006	A=0.559	G=0.441
1000Genomes	Global	Study-wide	5008	A=0.418	G=0.582
1000Genomes	South Asian	Sub	978	A=0.500	G=0.500
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.576	G=0.424
The Genome Aggregation Database	African	Sub	8712	A=0.338	G=0.662
The Genome Aggregation Database	American	Sub	838	A=0.450	G=0.550
The Genome Aggregation Database	East Asian	Sub	1612	A=0.266	G=0.734
The Genome Aggregation Database	Europe	Sub	18460	A=0.544	G=0.456
The Genome Aggregation Database	Global	Study-wide	29924	A=0.465	G=0.534
The Genome Aggregation Database	Other	Sub	302	A=0.430	G=0.570
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.442	G=0.557
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.562	G=0.438

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs531454	0.000522	alcohol dependence	20201924

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

Probe ID	Position	Gene	beta	p-value
cg24088508	chr1:38156462	C1orf109	-0.0810051130183631	5.4737e-12
cg12339802	chr1:38156545	C1orf109	-0.0821693326106414	1.8664e-9
cg22449745	chr1:38156939	C1orf109\|CDCA8	0.0316343700377182	2.1886e-9

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	38187361	38187574	E067	13764
chr1	38191964	38192177	E067	18367
chr1	38192582	38192688	E067	18985
chr1	38154757	38154919	E068	-18678
chr1	38187361	38187574	E068	13764
chr1	38189011	38189061	E068	15414
chr1	38192582	38192688	E068	18985
chr1	38141728	38141785	E069	-31812
chr1	38154757	38154919	E069	-18678
chr1	38187361	38187574	E069	13764
chr1	38189011	38189061	E069	15414
chr1	38189109	38189500	E069	15512
chr1	38191964	38192177	E069	18367
chr1	38192582	38192688	E069	18985
chr1	38154757	38154919	E070	-18678
chr1	38141421	38141471	E071	-32126
chr1	38154757	38154919	E071	-18678
chr1	38187361	38187574	E071	13764
chr1	38189011	38189061	E071	15414
chr1	38189109	38189500	E071	15512
chr1	38191964	38192177	E071	18367
chr1	38192582	38192688	E071	18985
chr1	38154757	38154919	E072	-18678
chr1	38187361	38187574	E072	13764
chr1	38189011	38189061	E072	15414
chr1	38191964	38192177	E072	18367
chr1	38192582	38192688	E072	18985
chr1	38154757	38154919	E073	-18678
chr1	38187361	38187574	E073	13764
chr1	38191964	38192177	E073	18367
chr1	38192582	38192688	E073	18985
chr1	38141421	38141471	E074	-32126
chr1	38154757	38154919	E074	-18678
chr1	38187361	38187574	E074	13764
chr1	38189011	38189061	E074	15414
chr1	38189109	38189500	E074	15512
chr1	38189548	38189624	E074	15951
chr1	38191964	38192177	E074	18367
chr1	38192582	38192688	E074	18985
chr1	38141421	38141471	E081	-32126
chr1	38141728	38141785	E081	-31812
chr1	38141998	38142657	E081	-30940
chr1	38154133	38154200	E081	-19397
chr1	38154757	38154919	E081	-18678
chr1	38191964	38192177	E081	18367
chr1	38192582	38192688	E081	18985
chr1	38191964	38192177	E082	18367
chr1	38192582	38192688	E082	18985

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	38155853	38156893	E067	-16704
chr1	38156949	38158763	E067	-14834
chr1	38218201	38218327	E067	44604
chr1	38218368	38218429	E067	44771
chr1	38218607	38218681	E067	45010
chr1	38218704	38218958	E067	45107
chr1	38155853	38156893	E068	-16704
chr1	38156949	38158763	E068	-14834
chr1	38218201	38218327	E068	44604
chr1	38218368	38218429	E068	44771
chr1	38218607	38218681	E068	45010
chr1	38218704	38218958	E068	45107
chr1	38155853	38156893	E069	-16704
chr1	38156949	38158763	E069	-14834
chr1	38218368	38218429	E069	44771
chr1	38218607	38218681	E069	45010
chr1	38218704	38218958	E069	45107
chr1	38155853	38156893	E070	-16704
chr1	38156949	38158763	E070	-14834
chr1	38218201	38218327	E070	44604
chr1	38218368	38218429	E070	44771
chr1	38218607	38218681	E070	45010
chr1	38218704	38218958	E070	45107
chr1	38155853	38156893	E071	-16704
chr1	38156949	38158763	E071	-14834
chr1	38218704	38218958	E071	45107
chr1	38155853	38156893	E072	-16704
chr1	38156949	38158763	E072	-14834
chr1	38218201	38218327	E072	44604
chr1	38218368	38218429	E072	44771
chr1	38218607	38218681	E072	45010
chr1	38218704	38218958	E072	45107
chr1	38155853	38156893	E073	-16704
chr1	38156949	38158763	E073	-14834
chr1	38218201	38218327	E073	44604
chr1	38218368	38218429	E073	44771
chr1	38218607	38218681	E073	45010
chr1	38218704	38218958	E073	45107
chr1	38155853	38156893	E074	-16704
chr1	38156949	38158763	E074	-14834
chr1	38155853	38156893	E081	-16704
chr1	38218201	38218327	E081	44604
chr1	38218368	38218429	E081	44771
chr1	38155853	38156893	E082	-16704
chr1	38156949	38158763	E082	-14834
chr1	38218201	38218327	E082	44604
chr1	38218368	38218429	E082	44771
chr1	38218607	38218681	E082	45010
chr1	38218704	38218958	E082	45107