rs284295

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 (8275/29868,GnomAD)
G=0308 (8984/29118,TOPMED)
G=0320 (1601/5008,1000G)
G=0168 (646/3854,ALSPAC)
G=0186 (690/3708,TWINSUK)

Position: chr1:10652040 (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.10652040A>G
GRCh37.p13 chr 1	NC_000001.10:g.10712097A>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=0.763	G=0.237
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
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
rs284295	1.37E-06	alcohol dependence (age at onset)	24962325

eQTL of rs284295 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 rs284295 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	-37406
chr1	10676080	10676130	E067	-35967
chr1	10676190	10676279	E067	-35818
chr1	10723387	10724295	E067	11290
chr1	10725989	10726476	E067	13892
chr1	10674618	10674691	E068	-37406
chr1	10723387	10724295	E068	11290
chr1	10674618	10674691	E069	-37406
chr1	10676080	10676130	E069	-35967
chr1	10676190	10676279	E069	-35818
chr1	10723387	10724295	E069	11290
chr1	10725626	10725944	E069	13529
chr1	10725989	10726476	E069	13892
chr1	10755770	10755982	E069	43673
chr1	10675435	10675632	E070	-36465
chr1	10676080	10676130	E070	-35967
chr1	10676190	10676279	E070	-35818
chr1	10676383	10676433	E070	-35664
chr1	10683745	10683802	E070	-28295
chr1	10692059	10692263	E070	-19834
chr1	10692491	10692700	E070	-19397
chr1	10692869	10693116	E070	-18981
chr1	10694645	10695194	E070	-16903
chr1	10695242	10696319	E070	-15778
chr1	10699890	10700675	E070	-11422
chr1	10700718	10700866	E070	-11231
chr1	10700912	10701033	E070	-11064
chr1	10701085	10701135	E070	-10962
chr1	10701359	10701479	E070	-10618
chr1	10708766	10708816	E070	-3281
chr1	10711529	10711737	E070	-360
chr1	10711855	10712174	E070	0
chr1	10723007	10723313	E070	10910
chr1	10723387	10724295	E070	11290
chr1	10724441	10724697	E070	12344
chr1	10730791	10730871	E070	18694
chr1	10731201	10731514	E070	19104
chr1	10731564	10731686	E070	19467
chr1	10731720	10732119	E070	19623
chr1	10733491	10733680	E070	21394
chr1	10734074	10734134	E070	21977
chr1	10734771	10734824	E070	22674
chr1	10735138	10735403	E070	23041
chr1	10735523	10735640	E070	23426
chr1	10737231	10738061	E070	25134
chr1	10738134	10738259	E070	26037
chr1	10738329	10738466	E070	26232
chr1	10738761	10738860	E070	26664
chr1	10738967	10740291	E070	26870
chr1	10674173	10674224	E071	-37873
chr1	10674618	10674691	E071	-37406
chr1	10675435	10675632	E071	-36465
chr1	10676080	10676130	E071	-35967
chr1	10676190	10676279	E071	-35818
chr1	10694645	10695194	E071	-16903
chr1	10695242	10696319	E071	-15778
chr1	10700718	10700866	E071	-11231
chr1	10700912	10701033	E071	-11064
chr1	10701085	10701135	E071	-10962
chr1	10723007	10723313	E071	10910
chr1	10723387	10724295	E071	11290
chr1	10725626	10725944	E071	13529
chr1	10725989	10726476	E071	13892
chr1	10742209	10742367	E071	30112
chr1	10674618	10674691	E072	-37406
chr1	10676080	10676130	E072	-35967
chr1	10676190	10676279	E072	-35818
chr1	10723007	10723313	E072	10910
chr1	10723387	10724295	E072	11290
chr1	10724441	10724697	E072	12344
chr1	10725626	10725944	E072	13529
chr1	10725989	10726476	E072	13892
chr1	10694645	10695194	E073	-16903
chr1	10723007	10723313	E073	10910
chr1	10723387	10724295	E073	11290
chr1	10674618	10674691	E074	-37406
chr1	10723387	10724295	E074	11290
chr1	10725626	10725944	E074	13529
chr1	10725989	10726476	E074	13892
chr1	10726487	10726755	E074	14390
chr1	10672536	10673120	E081	-38977
chr1	10675435	10675632	E081	-36465
chr1	10676080	10676130	E081	-35967
chr1	10676190	10676279	E081	-35818
chr1	10676383	10676433	E081	-35664
chr1	10695242	10696319	E081	-15778
chr1	10699890	10700675	E081	-11422
chr1	10700718	10700866	E081	-11231
chr1	10700912	10701033	E081	-11064
chr1	10711529	10711737	E081	-360
chr1	10711855	10712174	E081	0
chr1	10722583	10722820	E081	10486
chr1	10722892	10722989	E081	10795
chr1	10723007	10723313	E081	10910
chr1	10723387	10724295	E081	11290
chr1	10724441	10724697	E081	12344
chr1	10731201	10731514	E081	19104
chr1	10731564	10731686	E081	19467
chr1	10731720	10732119	E081	19623
chr1	10733491	10733680	E081	21394
chr1	10737231	10738061	E081	25134
chr1	10738134	10738259	E081	26037
chr1	10738329	10738466	E081	26232
chr1	10738761	10738860	E081	26664
chr1	10738967	10740291	E081	26870
chr1	10742209	10742367	E081	30112
chr1	10742504	10743011	E081	30407
chr1	10743017	10743352	E081	30920
chr1	10743354	10743692	E081	31257
chr1	10675435	10675632	E082	-36465
chr1	10694645	10695194	E082	-16903
chr1	10695242	10696319	E082	-15778
chr1	10723387	10724295	E082	11290
chr1	10724441	10724697	E082	12344
chr1	10738134	10738259	E082	26037
chr1	10738329	10738466	E082	26232
chr1	10738761	10738860	E082	26664
chr1	10742504	10743011	E082	30407
chr1	10743776	10743895	E082	31679

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10753063	10755583	E067	40966
chr1	10753063	10755583	E068	40966
chr1	10755595	10755720	E068	43498
chr1	10753063	10755583	E069	40966
chr1	10755595	10755720	E069	43498
chr1	10698813	10698918	E070	-13179
chr1	10698970	10699106	E070	-12991
chr1	10699129	10699276	E070	-12821
chr1	10753063	10755583	E070	40966
chr1	10755595	10755720	E070	43498
chr1	10753063	10755583	E071	40966
chr1	10755595	10755720	E071	43498
chr1	10753063	10755583	E072	40966
chr1	10755595	10755720	E072	43498
chr1	10753063	10755583	E073	40966
chr1	10755595	10755720	E073	43498
chr1	10753063	10755583	E074	40966
chr1	10698304	10698417	E082	-13680
chr1	10698437	10698582	E082	-13515
chr1	10698617	10698657	E082	-13440
chr1	10698725	10698803	E082	-13294
chr1	10698813	10698918	E082	-13179
chr1	10698970	10699106	E082	-12991
chr1	10699129	10699276	E082	-12821
chr1	10753063	10755583	E082	40966
chr1	10755595	10755720	E082	43498