rs284243

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CASZ1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0292 (8749/29880,GnomAD)
G=0331 (9645/29118,TOPMED)
G=0332 (1663/5008,1000G)
G=0169 (652/3854,ALSPAC)
G=0189 (701/3708,TWINSUK)

Position: chr1:10645823 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 131 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.10645823A>G
GRCh37.p13 chr 1	NC_000001.10:g.10705880A>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	Genic Downstream Transcript Variant
CASZ1 transcript variant X4	XM_005263479.3: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
CASZ1 transcript variant X5	XM_011541635.2:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.443	G=0.557
1000Genomes	American	Sub	694	A=0.800	G=0.200
1000Genomes	East Asian	Sub	1008	A=0.758	G=0.242
1000Genomes	Europe	Sub	1006	A=0.793	G=0.207
1000Genomes	Global	Study-wide	5008	A=0.668	G=0.332
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=0.831	G=0.169
The Genome Aggregation Database	African	Sub	8686	A=0.512	G=0.488
The Genome Aggregation Database	American	Sub	836	A=0.810	G=0.190
The Genome Aggregation Database	East Asian	Sub	1616	A=0.746	G=0.254
The Genome Aggregation Database	Europe	Sub	18440	A=0.790	G=0.209
The Genome Aggregation Database	Global	Study-wide	29880	A=0.707	G=0.292
The Genome Aggregation Database	Other	Sub	302	A=0.750	G=0.250
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.668	G=0.331
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.811	G=0.189

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
rs284243	2.9E-06	alcohol dependence (age at onset)	24962325

eQTL of rs284243 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 rs284243 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg18878351	chr1:10709343	CASZ1	-0.0437698917950508	6.5771e-12

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	-31189
chr1	10676080	10676130	E067	-29750
chr1	10676190	10676279	E067	-29601
chr1	10723387	10724295	E067	17507
chr1	10725989	10726476	E067	20109
chr1	10658122	10658519	E068	-47361
chr1	10674618	10674691	E068	-31189
chr1	10723387	10724295	E068	17507
chr1	10674618	10674691	E069	-31189
chr1	10676080	10676130	E069	-29750
chr1	10676190	10676279	E069	-29601
chr1	10723387	10724295	E069	17507
chr1	10725626	10725944	E069	19746
chr1	10725989	10726476	E069	20109
chr1	10657285	10657517	E070	-48363
chr1	10657636	10657777	E070	-48103
chr1	10657802	10657902	E070	-47978
chr1	10658122	10658519	E070	-47361
chr1	10658521	10658674	E070	-47206
chr1	10658819	10658900	E070	-46980
chr1	10659286	10659975	E070	-45905
chr1	10675435	10675632	E070	-30248
chr1	10676080	10676130	E070	-29750
chr1	10676190	10676279	E070	-29601
chr1	10676383	10676433	E070	-29447
chr1	10683745	10683802	E070	-22078
chr1	10692059	10692263	E070	-13617
chr1	10692491	10692700	E070	-13180
chr1	10692869	10693116	E070	-12764
chr1	10694645	10695194	E070	-10686
chr1	10695242	10696319	E070	-9561
chr1	10699890	10700675	E070	-5205
chr1	10700718	10700866	E070	-5014
chr1	10700912	10701033	E070	-4847
chr1	10701085	10701135	E070	-4745
chr1	10701359	10701479	E070	-4401
chr1	10708766	10708816	E070	2886
chr1	10711529	10711737	E070	5649
chr1	10711855	10712174	E070	5975
chr1	10723007	10723313	E070	17127
chr1	10723387	10724295	E070	17507
chr1	10724441	10724697	E070	18561
chr1	10730791	10730871	E070	24911
chr1	10731201	10731514	E070	25321
chr1	10731564	10731686	E070	25684
chr1	10731720	10732119	E070	25840
chr1	10733491	10733680	E070	27611
chr1	10734074	10734134	E070	28194
chr1	10734771	10734824	E070	28891
chr1	10735138	10735403	E070	29258
chr1	10735523	10735640	E070	29643
chr1	10737231	10738061	E070	31351
chr1	10738134	10738259	E070	32254
chr1	10738329	10738466	E070	32449
chr1	10738761	10738860	E070	32881
chr1	10738967	10740291	E070	33087
chr1	10658122	10658519	E071	-47361
chr1	10658521	10658674	E071	-47206
chr1	10674173	10674224	E071	-31656
chr1	10674618	10674691	E071	-31189
chr1	10675435	10675632	E071	-30248
chr1	10676080	10676130	E071	-29750
chr1	10676190	10676279	E071	-29601
chr1	10694645	10695194	E071	-10686
chr1	10695242	10696319	E071	-9561
chr1	10700718	10700866	E071	-5014
chr1	10700912	10701033	E071	-4847
chr1	10701085	10701135	E071	-4745
chr1	10723007	10723313	E071	17127
chr1	10723387	10724295	E071	17507
chr1	10725626	10725944	E071	19746
chr1	10725989	10726476	E071	20109
chr1	10742209	10742367	E071	36329
chr1	10658122	10658519	E072	-47361
chr1	10674618	10674691	E072	-31189
chr1	10676080	10676130	E072	-29750
chr1	10676190	10676279	E072	-29601
chr1	10723007	10723313	E072	17127
chr1	10723387	10724295	E072	17507
chr1	10724441	10724697	E072	18561
chr1	10725626	10725944	E072	19746
chr1	10725989	10726476	E072	20109
chr1	10658122	10658519	E073	-47361
chr1	10694645	10695194	E073	-10686
chr1	10723007	10723313	E073	17127
chr1	10723387	10724295	E073	17507
chr1	10658122	10658519	E074	-47361
chr1	10674618	10674691	E074	-31189
chr1	10723387	10724295	E074	17507
chr1	10725626	10725944	E074	19746
chr1	10725989	10726476	E074	20109
chr1	10726487	10726755	E074	20607
chr1	10672536	10673120	E081	-32760
chr1	10675435	10675632	E081	-30248
chr1	10676080	10676130	E081	-29750
chr1	10676190	10676279	E081	-29601
chr1	10676383	10676433	E081	-29447
chr1	10695242	10696319	E081	-9561
chr1	10699890	10700675	E081	-5205
chr1	10700718	10700866	E081	-5014
chr1	10700912	10701033	E081	-4847
chr1	10711529	10711737	E081	5649
chr1	10711855	10712174	E081	5975
chr1	10722583	10722820	E081	16703
chr1	10722892	10722989	E081	17012
chr1	10723007	10723313	E081	17127
chr1	10723387	10724295	E081	17507
chr1	10724441	10724697	E081	18561
chr1	10731201	10731514	E081	25321
chr1	10731564	10731686	E081	25684
chr1	10731720	10732119	E081	25840
chr1	10733491	10733680	E081	27611
chr1	10737231	10738061	E081	31351
chr1	10738134	10738259	E081	32254
chr1	10738329	10738466	E081	32449
chr1	10738761	10738860	E081	32881
chr1	10738967	10740291	E081	33087
chr1	10742209	10742367	E081	36329
chr1	10742504	10743011	E081	36624
chr1	10743017	10743352	E081	37137
chr1	10743354	10743692	E081	37474
chr1	10675435	10675632	E082	-30248
chr1	10694645	10695194	E082	-10686
chr1	10695242	10696319	E082	-9561
chr1	10723387	10724295	E082	17507
chr1	10724441	10724697	E082	18561
chr1	10738134	10738259	E082	32254
chr1	10738329	10738466	E082	32449
chr1	10738761	10738860	E082	32881
chr1	10742504	10743011	E082	36624
chr1	10743776	10743895	E082	37896

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10753063	10755583	E067	47183
chr1	10753063	10755583	E068	47183
chr1	10755595	10755720	E068	49715
chr1	10753063	10755583	E069	47183
chr1	10755595	10755720	E069	49715
chr1	10698813	10698918	E070	-6962
chr1	10698970	10699106	E070	-6774
chr1	10699129	10699276	E070	-6604
chr1	10753063	10755583	E070	47183
chr1	10755595	10755720	E070	49715
chr1	10753063	10755583	E071	47183
chr1	10755595	10755720	E071	49715
chr1	10753063	10755583	E072	47183
chr1	10755595	10755720	E072	49715
chr1	10753063	10755583	E073	47183
chr1	10755595	10755720	E073	49715
chr1	10753063	10755583	E074	47183
chr1	10698304	10698417	E082	-7463
chr1	10698437	10698582	E082	-7298
chr1	10698617	10698657	E082	-7223
chr1	10698725	10698803	E082	-7077
chr1	10698813	10698918	E082	-6962
chr1	10698970	10699106	E082	-6774
chr1	10699129	10699276	E082	-6604
chr1	10753063	10755583	E082	47183
chr1	10755595	10755720	E082	49715