rs12564594

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ZNF648 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0047 (1427/29980,GnomAD)
G=0030 (876/29118,TOPMED)
G=0080 (401/5008,1000G)
G=0035 (136/3854,ALSPAC)
G=0034 (127/3708,TWINSUK)

Position: chr1:182147233 (GRCh38.p7) (1q25.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 157 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.182147233A>G
GRCh37.p13 chr 1	NC_000001.10:g.182116368A>G

Gene: ZNF648, zinc finger protein 648(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF648 transcript	NM_001009992.1:c.	N/A	Genic Upstream Transcript Variant
ZNF648 transcript variant X2	XM_017000302.1:c.	N/A	Intron Variant
ZNF648 transcript variant X1	XM_017000301.1:c.	N/A	Genic Upstream Transcript Variant
ZNF648 transcript variant X3	XR_001736975.1:n.	N/A	Genic Downstream Transcript Variant
ZNF648 transcript variant X4	XR_001736976.1:n.	N/A	Genic Downstream Transcript Variant
ZNF648 transcript variant X5	XR_001736977.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.990	G=0.010
1000Genomes	American	Sub	694	A=0.950	G=0.050
1000Genomes	East Asian	Sub	1008	A=0.767	G=0.233
1000Genomes	Europe	Sub	1006	A=0.960	G=0.040
1000Genomes	Global	Study-wide	5008	A=0.920	G=0.080
1000Genomes	South Asian	Sub	978	A=0.920	G=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.965	G=0.035
The Genome Aggregation Database	African	Sub	8728	A=0.987	G=0.013
The Genome Aggregation Database	American	Sub	838	A=0.940	G=0.060
The Genome Aggregation Database	East Asian	Sub	1616	A=0.788	G=0.212
The Genome Aggregation Database	Europe	Sub	18496	A=0.950	G=0.049
The Genome Aggregation Database	Global	Study-wide	29980	A=0.952	G=0.047
The Genome Aggregation Database	Other	Sub	302	A=0.970	G=0.030
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.969	G=0.030
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.966	G=0.034

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
rs12564594	0.000392	alcohol dependence	20201924

eQTL of rs12564594 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 rs12564594 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 )
chr1	182089648	182090293	E067	-26075
chr1	182090331	182090411	E067	-25957
chr1	182090892	182091160	E067	-25208
chr1	182091226	182091283	E067	-25085
chr1	182091428	182091962	E067	-24406
chr1	182111690	182111840	E067	-4528
chr1	182112110	182112195	E067	-4173
chr1	182112245	182114514	E067	-1854
chr1	182114639	182114996	E067	-1372
chr1	182115092	182115185	E067	-1183
chr1	182115241	182115433	E067	-935
chr1	182115449	182115743	E067	-625
chr1	182132617	182132732	E067	16249
chr1	182132791	182133418	E067	16423
chr1	182133535	182133751	E067	17167
chr1	182158650	182158952	E067	42282
chr1	182082999	182083160	E068	-33208
chr1	182083243	182083310	E068	-33058
chr1	182083376	182083726	E068	-32642
chr1	182083899	182084153	E068	-32215
chr1	182089648	182090293	E068	-26075
chr1	182090331	182090411	E068	-25957
chr1	182090892	182091160	E068	-25208
chr1	182091226	182091283	E068	-25085
chr1	182091428	182091962	E068	-24406
chr1	182106093	182106143	E068	-10225
chr1	182106288	182106414	E068	-9954
chr1	182111690	182111840	E068	-4528
chr1	182112110	182112195	E068	-4173
chr1	182112245	182114514	E068	-1854
chr1	182114639	182114996	E068	-1372
chr1	182115092	182115185	E068	-1183
chr1	182115241	182115433	E068	-935
chr1	182132617	182132732	E068	16249
chr1	182132791	182133418	E068	16423
chr1	182133535	182133751	E068	17167
chr1	182133912	182133974	E068	17544
chr1	182156035	182156130	E068	39667
chr1	182089648	182090293	E069	-26075
chr1	182090331	182090411	E069	-25957
chr1	182090892	182091160	E069	-25208
chr1	182091226	182091283	E069	-25085
chr1	182106288	182106414	E069	-9954
chr1	182110218	182110503	E069	-5865
chr1	182112110	182112195	E069	-4173
chr1	182112245	182114514	E069	-1854
chr1	182114639	182114996	E069	-1372
chr1	182115092	182115185	E069	-1183
chr1	182115241	182115433	E069	-935
chr1	182115449	182115743	E069	-625
chr1	182132617	182132732	E069	16249
chr1	182132791	182133418	E069	16423
chr1	182133535	182133751	E069	17167
chr1	182143380	182143945	E069	27012
chr1	182144527	182145313	E069	28159
chr1	182158650	182158952	E069	42282
chr1	182112245	182114514	E070	-1854
chr1	182079904	182080031	E071	-36337
chr1	182080731	182080885	E071	-35483
chr1	182090892	182091160	E071	-25208
chr1	182091226	182091283	E071	-25085
chr1	182091428	182091962	E071	-24406
chr1	182112110	182112195	E071	-4173
chr1	182112245	182114514	E071	-1854
chr1	182114639	182114996	E071	-1372
chr1	182115092	182115185	E071	-1183
chr1	182115241	182115433	E071	-935
chr1	182115449	182115743	E071	-625
chr1	182118094	182118311	E071	1726
chr1	182132617	182132732	E071	16249
chr1	182132791	182133418	E071	16423
chr1	182133535	182133751	E071	17167
chr1	182133912	182133974	E071	17544
chr1	182142211	182142261	E071	25843
chr1	182142373	182142471	E071	26005
chr1	182142580	182142714	E071	26212
chr1	182142994	182143370	E071	26626
chr1	182143380	182143945	E071	27012
chr1	182144527	182145313	E071	28159
chr1	182083376	182083726	E072	-32642
chr1	182083899	182084153	E072	-32215
chr1	182089648	182090293	E072	-26075
chr1	182090331	182090411	E072	-25957
chr1	182090892	182091160	E072	-25208
chr1	182091226	182091283	E072	-25085
chr1	182091428	182091962	E072	-24406
chr1	182111690	182111840	E072	-4528
chr1	182112110	182112195	E072	-4173
chr1	182112245	182114514	E072	-1854
chr1	182114639	182114996	E072	-1372
chr1	182132617	182132732	E072	16249
chr1	182132791	182133418	E072	16423
chr1	182133535	182133751	E072	17167
chr1	182133912	182133974	E072	17544
chr1	182135493	182135684	E072	19125
chr1	182135695	182135746	E072	19327
chr1	182135894	182135980	E072	19526
chr1	182142994	182143370	E072	26626
chr1	182143380	182143945	E072	27012
chr1	182155564	182155747	E072	39196
chr1	182082999	182083160	E073	-33208
chr1	182083243	182083310	E073	-33058
chr1	182083376	182083726	E073	-32642
chr1	182083899	182084153	E073	-32215
chr1	182089648	182090293	E073	-26075
chr1	182090331	182090411	E073	-25957
chr1	182090892	182091160	E073	-25208
chr1	182091226	182091283	E073	-25085
chr1	182111356	182111406	E073	-4962
chr1	182111690	182111840	E073	-4528
chr1	182112110	182112195	E073	-4173
chr1	182112245	182114514	E073	-1854
chr1	182114639	182114996	E073	-1372
chr1	182132617	182132732	E073	16249
chr1	182132791	182133418	E073	16423
chr1	182133535	182133751	E073	17167
chr1	182133912	182133974	E073	17544
chr1	182142994	182143370	E073	26626
chr1	182143380	182143945	E073	27012
chr1	182144527	182145313	E073	28159
chr1	182082999	182083160	E074	-33208
chr1	182083243	182083310	E074	-33058
chr1	182083376	182083726	E074	-32642
chr1	182089648	182090293	E074	-26075
chr1	182090331	182090411	E074	-25957
chr1	182090892	182091160	E074	-25208
chr1	182091226	182091283	E074	-25085
chr1	182091428	182091962	E074	-24406
chr1	182111690	182111840	E074	-4528
chr1	182112110	182112195	E074	-4173
chr1	182112245	182114514	E074	-1854
chr1	182114639	182114996	E074	-1372
chr1	182115092	182115185	E074	-1183
chr1	182115241	182115433	E074	-935
chr1	182118094	182118311	E074	1726
chr1	182132617	182132732	E074	16249
chr1	182132791	182133418	E074	16423
chr1	182133535	182133751	E074	17167
chr1	182135695	182135746	E074	19327
chr1	182135894	182135980	E074	19526
chr1	182142994	182143370	E074	26626
chr1	182143380	182143945	E074	27012
chr1	182082999	182083160	E081	-33208
chr1	182083243	182083310	E081	-33058
chr1	182083376	182083726	E081	-32642
chr1	182089648	182090293	E081	-26075
chr1	182090331	182090411	E081	-25957
chr1	182142373	182142471	E081	26005
chr1	182142580	182142714	E081	26212
chr1	182142994	182143370	E081	26626
chr1	182082999	182083160	E082	-33208
chr1	182083243	182083310	E082	-33058
chr1	182083376	182083726	E082	-32642
chr1	182142373	182142471	E082	26005
chr1	182142580	182142714	E082	26212
chr1	182142994	182143370	E082	26626
chr1	182143380	182143945	E082	27012