rs284298

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CASZ1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0267 (8002/29890,GnomAD)
A=0309 (9021/29118,TOPMED)
A=0313 (1566/5008,1000G)
A=0156 (601/3854,ALSPAC)
A=0173 (643/3708,TWINSUK)

Position: chr1:10650198 (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.10650198G>A
GRCh37.p13 chr 1	NC_000001.10:g.10710255G>A

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	G=0.458	A=0.542
1000Genomes	American	Sub	694	G=0.860	A=0.140
1000Genomes	East Asian	Sub	1008	G=0.769	A=0.231
1000Genomes	Europe	Sub	1006	G=0.817	A=0.183
1000Genomes	Global	Study-wide	5008	G=0.687	A=0.313
1000Genomes	South Asian	Sub	978	G=0.660	A=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.844	A=0.156
The Genome Aggregation Database	African	Sub	8694	G=0.523	A=0.477
The Genome Aggregation Database	American	Sub	838	G=0.880	A=0.120
The Genome Aggregation Database	East Asian	Sub	1616	G=0.770	A=0.230
The Genome Aggregation Database	Europe	Sub	18440	G=0.820	A=0.179
The Genome Aggregation Database	Global	Study-wide	29890	G=0.732	A=0.267
The Genome Aggregation Database	Other	Sub	302	G=0.770	A=0.230
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.690	A=0.309
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.827	A=0.173

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
rs284298	8.55E-06	alcohol dependence (age at onset)	24962325

eQTL of rs284298 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 rs284298 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg18878351	chr1:10709343	CASZ1	-0.046937033000209	1.3815e-13

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	-35564
chr1	10676080	10676130	E067	-34125
chr1	10676190	10676279	E067	-33976
chr1	10723387	10724295	E067	13132
chr1	10725989	10726476	E067	15734
chr1	10674618	10674691	E068	-35564
chr1	10723387	10724295	E068	13132
chr1	10674618	10674691	E069	-35564
chr1	10676080	10676130	E069	-34125
chr1	10676190	10676279	E069	-33976
chr1	10723387	10724295	E069	13132
chr1	10725626	10725944	E069	15371
chr1	10725989	10726476	E069	15734
chr1	10755770	10755982	E069	45515
chr1	10675435	10675632	E070	-34623
chr1	10676080	10676130	E070	-34125
chr1	10676190	10676279	E070	-33976
chr1	10676383	10676433	E070	-33822
chr1	10683745	10683802	E070	-26453
chr1	10692059	10692263	E070	-17992
chr1	10692491	10692700	E070	-17555
chr1	10692869	10693116	E070	-17139
chr1	10694645	10695194	E070	-15061
chr1	10695242	10696319	E070	-13936
chr1	10699890	10700675	E070	-9580
chr1	10700718	10700866	E070	-9389
chr1	10700912	10701033	E070	-9222
chr1	10701085	10701135	E070	-9120
chr1	10701359	10701479	E070	-8776
chr1	10708766	10708816	E070	-1439
chr1	10711529	10711737	E070	1274
chr1	10711855	10712174	E070	1600
chr1	10723007	10723313	E070	12752
chr1	10723387	10724295	E070	13132
chr1	10724441	10724697	E070	14186
chr1	10730791	10730871	E070	20536
chr1	10731201	10731514	E070	20946
chr1	10731564	10731686	E070	21309
chr1	10731720	10732119	E070	21465
chr1	10733491	10733680	E070	23236
chr1	10734074	10734134	E070	23819
chr1	10734771	10734824	E070	24516
chr1	10735138	10735403	E070	24883
chr1	10735523	10735640	E070	25268
chr1	10737231	10738061	E070	26976
chr1	10738134	10738259	E070	27879
chr1	10738329	10738466	E070	28074
chr1	10738761	10738860	E070	28506
chr1	10738967	10740291	E070	28712
chr1	10674173	10674224	E071	-36031
chr1	10674618	10674691	E071	-35564
chr1	10675435	10675632	E071	-34623
chr1	10676080	10676130	E071	-34125
chr1	10676190	10676279	E071	-33976
chr1	10694645	10695194	E071	-15061
chr1	10695242	10696319	E071	-13936
chr1	10700718	10700866	E071	-9389
chr1	10700912	10701033	E071	-9222
chr1	10701085	10701135	E071	-9120
chr1	10723007	10723313	E071	12752
chr1	10723387	10724295	E071	13132
chr1	10725626	10725944	E071	15371
chr1	10725989	10726476	E071	15734
chr1	10742209	10742367	E071	31954
chr1	10674618	10674691	E072	-35564
chr1	10676080	10676130	E072	-34125
chr1	10676190	10676279	E072	-33976
chr1	10723007	10723313	E072	12752
chr1	10723387	10724295	E072	13132
chr1	10724441	10724697	E072	14186
chr1	10725626	10725944	E072	15371
chr1	10725989	10726476	E072	15734
chr1	10694645	10695194	E073	-15061
chr1	10723007	10723313	E073	12752
chr1	10723387	10724295	E073	13132
chr1	10674618	10674691	E074	-35564
chr1	10723387	10724295	E074	13132
chr1	10725626	10725944	E074	15371
chr1	10725989	10726476	E074	15734
chr1	10726487	10726755	E074	16232
chr1	10672536	10673120	E081	-37135
chr1	10675435	10675632	E081	-34623
chr1	10676080	10676130	E081	-34125
chr1	10676190	10676279	E081	-33976
chr1	10676383	10676433	E081	-33822
chr1	10695242	10696319	E081	-13936
chr1	10699890	10700675	E081	-9580
chr1	10700718	10700866	E081	-9389
chr1	10700912	10701033	E081	-9222
chr1	10711529	10711737	E081	1274
chr1	10711855	10712174	E081	1600
chr1	10722583	10722820	E081	12328
chr1	10722892	10722989	E081	12637
chr1	10723007	10723313	E081	12752
chr1	10723387	10724295	E081	13132
chr1	10724441	10724697	E081	14186
chr1	10731201	10731514	E081	20946
chr1	10731564	10731686	E081	21309
chr1	10731720	10732119	E081	21465
chr1	10733491	10733680	E081	23236
chr1	10737231	10738061	E081	26976
chr1	10738134	10738259	E081	27879
chr1	10738329	10738466	E081	28074
chr1	10738761	10738860	E081	28506
chr1	10738967	10740291	E081	28712
chr1	10742209	10742367	E081	31954
chr1	10742504	10743011	E081	32249
chr1	10743017	10743352	E081	32762
chr1	10743354	10743692	E081	33099
chr1	10675435	10675632	E082	-34623
chr1	10694645	10695194	E082	-15061
chr1	10695242	10696319	E082	-13936
chr1	10723387	10724295	E082	13132
chr1	10724441	10724697	E082	14186
chr1	10738134	10738259	E082	27879
chr1	10738329	10738466	E082	28074
chr1	10738761	10738860	E082	28506
chr1	10742504	10743011	E082	32249
chr1	10743776	10743895	E082	33521

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10753063	10755583	E067	42808
chr1	10753063	10755583	E068	42808
chr1	10755595	10755720	E068	45340
chr1	10753063	10755583	E069	42808
chr1	10755595	10755720	E069	45340
chr1	10698813	10698918	E070	-11337
chr1	10698970	10699106	E070	-11149
chr1	10699129	10699276	E070	-10979
chr1	10753063	10755583	E070	42808
chr1	10755595	10755720	E070	45340
chr1	10753063	10755583	E071	42808
chr1	10755595	10755720	E071	45340
chr1	10753063	10755583	E072	42808
chr1	10755595	10755720	E072	45340
chr1	10753063	10755583	E073	42808
chr1	10755595	10755720	E073	45340
chr1	10753063	10755583	E074	42808
chr1	10698304	10698417	E082	-11838
chr1	10698437	10698582	E082	-11673
chr1	10698617	10698657	E082	-11598
chr1	10698725	10698803	E082	-11452
chr1	10698813	10698918	E082	-11337
chr1	10698970	10699106	E082	-11149
chr1	10699129	10699276	E082	-10979
chr1	10753063	10755583	E082	42808
chr1	10755595	10755720	E082	45340