rs615530

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CDCA8 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0466 (13941/29918,GnomAD)
A==0443 (12902/29118,TOPMED)
A==0418 (2091/5008,1000G)
G=0482 (2201/4566,GO-ESP)
G=0424 (1634/3854,ALSPAC)
G=0438 (1624/3708,TWINSUK)

Position: chr1:37696022 (GRCh38.p7) (1p34.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 48 Enhancers around

Promoter: 19 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.37696022A>G
GRCh37.p13 chr 1	NC_000001.10:g.38161694A>G

Gene: CDCA8, cell division cycle associated 8(plus strand)

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.311	G=0.689
1000Genomes	American	Sub	694	A=0.480	G=0.520
1000Genomes	East Asian	Sub	1008	A=0.297	G=0.703
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	8704	A=0.339	G=0.661
The Genome Aggregation Database	American	Sub	834	A=0.450	G=0.550
The Genome Aggregation Database	East Asian	Sub	1616	A=0.267	G=0.733
The Genome Aggregation Database	Europe	Sub	18464	A=0.544	G=0.455
The Genome Aggregation Database	Global	Study-wide	29918	A=0.466	G=0.534
The Genome Aggregation Database	Other	Sub	300	A=0.430	G=0.570
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.443	G=0.556
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

P-Value

SNP ID	p-value	Traits	Study
rs615530	0.000841	alcohol dependence	20201924

eQTL of rs615530 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 rs615530 in Fetal Brain

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

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 )
chr1	38187361	38187574	E067	25667
chr1	38191964	38192177	E067	30270
chr1	38192582	38192688	E067	30888
chr1	38154757	38154919	E068	-6775
chr1	38187361	38187574	E068	25667
chr1	38189011	38189061	E068	27317
chr1	38192582	38192688	E068	30888
chr1	38141728	38141785	E069	-19909
chr1	38154757	38154919	E069	-6775
chr1	38187361	38187574	E069	25667
chr1	38189011	38189061	E069	27317
chr1	38189109	38189500	E069	27415
chr1	38191964	38192177	E069	30270
chr1	38192582	38192688	E069	30888
chr1	38154757	38154919	E070	-6775
chr1	38141421	38141471	E071	-20223
chr1	38154757	38154919	E071	-6775
chr1	38187361	38187574	E071	25667
chr1	38189011	38189061	E071	27317
chr1	38189109	38189500	E071	27415
chr1	38191964	38192177	E071	30270
chr1	38192582	38192688	E071	30888
chr1	38154757	38154919	E072	-6775
chr1	38187361	38187574	E072	25667
chr1	38189011	38189061	E072	27317
chr1	38191964	38192177	E072	30270
chr1	38192582	38192688	E072	30888
chr1	38154757	38154919	E073	-6775
chr1	38187361	38187574	E073	25667
chr1	38191964	38192177	E073	30270
chr1	38192582	38192688	E073	30888
chr1	38141421	38141471	E074	-20223
chr1	38154757	38154919	E074	-6775
chr1	38187361	38187574	E074	25667
chr1	38189011	38189061	E074	27317
chr1	38189109	38189500	E074	27415
chr1	38189548	38189624	E074	27854
chr1	38191964	38192177	E074	30270
chr1	38192582	38192688	E074	30888
chr1	38141421	38141471	E081	-20223
chr1	38141728	38141785	E081	-19909
chr1	38141998	38142657	E081	-19037
chr1	38154133	38154200	E081	-7494
chr1	38154757	38154919	E081	-6775
chr1	38191964	38192177	E081	30270
chr1	38192582	38192688	E081	30888
chr1	38191964	38192177	E082	30270
chr1	38192582	38192688	E082	30888

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	38155853	38156893	E067	-4801
chr1	38156949	38158763	E067	-2931
chr1	38155853	38156893	E068	-4801
chr1	38156949	38158763	E068	-2931
chr1	38155853	38156893	E069	-4801
chr1	38156949	38158763	E069	-2931
chr1	38155853	38156893	E070	-4801
chr1	38156949	38158763	E070	-2931
chr1	38155853	38156893	E071	-4801
chr1	38156949	38158763	E071	-2931
chr1	38155853	38156893	E072	-4801
chr1	38156949	38158763	E072	-2931
chr1	38155853	38156893	E073	-4801
chr1	38156949	38158763	E073	-2931
chr1	38155853	38156893	E074	-4801
chr1	38156949	38158763	E074	-2931
chr1	38155853	38156893	E081	-4801
chr1	38155853	38156893	E082	-4801
chr1	38156949	38158763	E082	-2931