rs284296

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CASZ1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0277 (8268/29846,GnomAD)
G=0308 (8981/29118,TOPMED)
G=0320 (1602/5008,1000G)
G=0168 (646/3854,ALSPAC)
G=0186 (690/3708,TWINSUK)

Position: chr1:10652032 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 119 Enhancers around

Promoter: 26 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.10652032A>G
GRCh37.p13 chr 1	NC_000001.10:g.10712089A>G

Gene: CASZ1, castor zinc finger 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CASZ1 transcript variant 1	NM_001079843.2:c.	N/A	Intron Variant
CASZ1 transcript variant 2	NM_017766.4:c.	N/A	Intron Variant
CASZ1 transcript variant X4	XM_005263479.3:c.	N/A	Intron Variant
CASZ1 transcript variant X5	XM_011541635.2:c.	N/A	Intron Variant
CASZ1 transcript variant X1	XM_017001539.1:c.	N/A	Intron Variant
CASZ1 transcript variant X2	XM_017001540.1:c.	N/A	Intron Variant
CASZ1 transcript variant X3	XM_017001541.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.486	G=0.514
1000Genomes	American	Sub	694	A=0.810	G=0.190
1000Genomes	East Asian	Sub	1008	A=0.762	G=0.238
1000Genomes	Europe	Sub	1006	A=0.792	G=0.208
1000Genomes	Global	Study-wide	5008	A=0.680	G=0.320
1000Genomes	South Asian	Sub	978	A=0.650	G=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.832	G=0.168
The Genome Aggregation Database	African	Sub	8644	A=0.561	G=0.439
The Genome Aggregation Database	American	Sub	838	A=0.810	G=0.190
The Genome Aggregation Database	East Asian	Sub	1618	A=0.754	G=0.246
The Genome Aggregation Database	Europe	Sub	18444	A=0.791	G=0.208
The Genome Aggregation Database	Global	Study-wide	29846	A=0.723	G=0.277
The Genome Aggregation Database	Other	Sub	302	A=0.760	G=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.691	G=0.308
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.814	G=0.186

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs284296	1.37E-06	alcohol dependence (age at onset)	24962325

eQTL of rs284296 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 rs284296 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg18878351	chr1:10709343	CASZ1	-0.0411492720609452	7.0340e-11

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	10674618	10674691	E067	-37398
chr1	10676080	10676130	E067	-35959
chr1	10676190	10676279	E067	-35810
chr1	10723387	10724295	E067	11298
chr1	10725989	10726476	E067	13900
chr1	10674618	10674691	E068	-37398
chr1	10723387	10724295	E068	11298
chr1	10674618	10674691	E069	-37398
chr1	10676080	10676130	E069	-35959
chr1	10676190	10676279	E069	-35810
chr1	10723387	10724295	E069	11298
chr1	10725626	10725944	E069	13537
chr1	10725989	10726476	E069	13900
chr1	10755770	10755982	E069	43681
chr1	10675435	10675632	E070	-36457
chr1	10676080	10676130	E070	-35959
chr1	10676190	10676279	E070	-35810
chr1	10676383	10676433	E070	-35656
chr1	10683745	10683802	E070	-28287
chr1	10692059	10692263	E070	-19826
chr1	10692491	10692700	E070	-19389
chr1	10692869	10693116	E070	-18973
chr1	10694645	10695194	E070	-16895
chr1	10695242	10696319	E070	-15770
chr1	10699890	10700675	E070	-11414
chr1	10700718	10700866	E070	-11223
chr1	10700912	10701033	E070	-11056
chr1	10701085	10701135	E070	-10954
chr1	10701359	10701479	E070	-10610
chr1	10708766	10708816	E070	-3273
chr1	10711529	10711737	E070	-352
chr1	10711855	10712174	E070	0
chr1	10723007	10723313	E070	10918
chr1	10723387	10724295	E070	11298
chr1	10724441	10724697	E070	12352
chr1	10730791	10730871	E070	18702
chr1	10731201	10731514	E070	19112
chr1	10731564	10731686	E070	19475
chr1	10731720	10732119	E070	19631
chr1	10733491	10733680	E070	21402
chr1	10734074	10734134	E070	21985
chr1	10734771	10734824	E070	22682
chr1	10735138	10735403	E070	23049
chr1	10735523	10735640	E070	23434
chr1	10737231	10738061	E070	25142
chr1	10738134	10738259	E070	26045
chr1	10738329	10738466	E070	26240
chr1	10738761	10738860	E070	26672
chr1	10738967	10740291	E070	26878
chr1	10674173	10674224	E071	-37865
chr1	10674618	10674691	E071	-37398
chr1	10675435	10675632	E071	-36457
chr1	10676080	10676130	E071	-35959
chr1	10676190	10676279	E071	-35810
chr1	10694645	10695194	E071	-16895
chr1	10695242	10696319	E071	-15770
chr1	10700718	10700866	E071	-11223
chr1	10700912	10701033	E071	-11056
chr1	10701085	10701135	E071	-10954
chr1	10723007	10723313	E071	10918
chr1	10723387	10724295	E071	11298
chr1	10725626	10725944	E071	13537
chr1	10725989	10726476	E071	13900
chr1	10742209	10742367	E071	30120
chr1	10674618	10674691	E072	-37398
chr1	10676080	10676130	E072	-35959
chr1	10676190	10676279	E072	-35810
chr1	10723007	10723313	E072	10918
chr1	10723387	10724295	E072	11298
chr1	10724441	10724697	E072	12352
chr1	10725626	10725944	E072	13537
chr1	10725989	10726476	E072	13900
chr1	10694645	10695194	E073	-16895
chr1	10723007	10723313	E073	10918
chr1	10723387	10724295	E073	11298
chr1	10674618	10674691	E074	-37398
chr1	10723387	10724295	E074	11298
chr1	10725626	10725944	E074	13537
chr1	10725989	10726476	E074	13900
chr1	10726487	10726755	E074	14398
chr1	10672536	10673120	E081	-38969
chr1	10675435	10675632	E081	-36457
chr1	10676080	10676130	E081	-35959
chr1	10676190	10676279	E081	-35810
chr1	10676383	10676433	E081	-35656
chr1	10695242	10696319	E081	-15770
chr1	10699890	10700675	E081	-11414
chr1	10700718	10700866	E081	-11223
chr1	10700912	10701033	E081	-11056
chr1	10711529	10711737	E081	-352
chr1	10711855	10712174	E081	0
chr1	10722583	10722820	E081	10494
chr1	10722892	10722989	E081	10803
chr1	10723007	10723313	E081	10918
chr1	10723387	10724295	E081	11298
chr1	10724441	10724697	E081	12352
chr1	10731201	10731514	E081	19112
chr1	10731564	10731686	E081	19475
chr1	10731720	10732119	E081	19631
chr1	10733491	10733680	E081	21402
chr1	10737231	10738061	E081	25142
chr1	10738134	10738259	E081	26045
chr1	10738329	10738466	E081	26240
chr1	10738761	10738860	E081	26672
chr1	10738967	10740291	E081	26878
chr1	10742209	10742367	E081	30120
chr1	10742504	10743011	E081	30415
chr1	10743017	10743352	E081	30928
chr1	10743354	10743692	E081	31265
chr1	10675435	10675632	E082	-36457
chr1	10694645	10695194	E082	-16895
chr1	10695242	10696319	E082	-15770
chr1	10723387	10724295	E082	11298
chr1	10724441	10724697	E082	12352
chr1	10738134	10738259	E082	26045
chr1	10738329	10738466	E082	26240
chr1	10738761	10738860	E082	26672
chr1	10742504	10743011	E082	30415
chr1	10743776	10743895	E082	31687

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10753063	10755583	E067	40974
chr1	10753063	10755583	E068	40974
chr1	10755595	10755720	E068	43506
chr1	10753063	10755583	E069	40974
chr1	10755595	10755720	E069	43506
chr1	10698813	10698918	E070	-13171
chr1	10698970	10699106	E070	-12983
chr1	10699129	10699276	E070	-12813
chr1	10753063	10755583	E070	40974
chr1	10755595	10755720	E070	43506
chr1	10753063	10755583	E071	40974
chr1	10755595	10755720	E071	43506
chr1	10753063	10755583	E072	40974
chr1	10755595	10755720	E072	43506
chr1	10753063	10755583	E073	40974
chr1	10755595	10755720	E073	43506
chr1	10753063	10755583	E074	40974
chr1	10698304	10698417	E082	-13672
chr1	10698437	10698582	E082	-13507
chr1	10698617	10698657	E082	-13432
chr1	10698725	10698803	E082	-13286
chr1	10698813	10698918	E082	-13171
chr1	10698970	10699106	E082	-12983
chr1	10699129	10699276	E082	-12813
chr1	10753063	10755583	E082	40974
chr1	10755595	10755720	E082	43506