rs284320

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CASZ1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0287 (8596/29884,GnomAD)
C=0317 (9254/29118,TOPMED)
C=0306 (1530/5008,1000G)
C=0184 (710/3854,ALSPAC)
C=0203 (754/3708,TWINSUK)

Position: chr1:10666963 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 125 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.10666963T>C
GRCh37.p13 chr 1	NC_000001.10:g.10727020T>C

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	T=0.495	C=0.505
1000Genomes	American	Sub	694	T=0.800	C=0.200
1000Genomes	East Asian	Sub	1008	T=0.819	C=0.181
1000Genomes	Europe	Sub	1006	T=0.781	C=0.219
1000Genomes	Global	Study-wide	5008	T=0.694	C=0.306
1000Genomes	South Asian	Sub	978	T=0.670	C=0.330
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.816	C=0.184
The Genome Aggregation Database	African	Sub	8698	T=0.552	C=0.448
The Genome Aggregation Database	American	Sub	836	T=0.810	C=0.190
The Genome Aggregation Database	East Asian	Sub	1620	T=0.791	C=0.209
The Genome Aggregation Database	Europe	Sub	18428	T=0.776	C=0.223
The Genome Aggregation Database	Global	Study-wide	29884	T=0.712	C=0.287
The Genome Aggregation Database	Other	Sub	302	T=0.750	C=0.250
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.682	C=0.317
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.797	C=0.203

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
21424828	The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA.	Chiang CW	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs284320	2.02E-06	alcohol dependence (age at onset)	24962325

eQTL of rs284320 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 rs284320 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg18878351	chr1:10709343	CASZ1	-0.0375564970627596	8.1391e-9

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	10723387	10724295	E067	-2725
chr1	10725989	10726476	E067	-544
chr1	10723387	10724295	E068	-2725
chr1	10723387	10724295	E069	-2725
chr1	10725626	10725944	E069	-1076
chr1	10725989	10726476	E069	-544
chr1	10755770	10755982	E069	28750
chr1	10683745	10683802	E070	-43218
chr1	10692059	10692263	E070	-34757
chr1	10692491	10692700	E070	-34320
chr1	10692869	10693116	E070	-33904
chr1	10694645	10695194	E070	-31826
chr1	10695242	10696319	E070	-30701
chr1	10699890	10700675	E070	-26345
chr1	10700718	10700866	E070	-26154
chr1	10700912	10701033	E070	-25987
chr1	10701085	10701135	E070	-25885
chr1	10701359	10701479	E070	-25541
chr1	10708766	10708816	E070	-18204
chr1	10711529	10711737	E070	-15283
chr1	10711855	10712174	E070	-14846
chr1	10723007	10723313	E070	-3707
chr1	10723387	10724295	E070	-2725
chr1	10724441	10724697	E070	-2323
chr1	10730791	10730871	E070	3771
chr1	10731201	10731514	E070	4181
chr1	10731564	10731686	E070	4544
chr1	10731720	10732119	E070	4700
chr1	10733491	10733680	E070	6471
chr1	10734074	10734134	E070	7054
chr1	10734771	10734824	E070	7751
chr1	10735138	10735403	E070	8118
chr1	10735523	10735640	E070	8503
chr1	10737231	10738061	E070	10211
chr1	10738134	10738259	E070	11114
chr1	10738329	10738466	E070	11309
chr1	10738761	10738860	E070	11741
chr1	10738967	10740291	E070	11947
chr1	10767361	10767513	E070	40341
chr1	10767551	10767643	E070	40531
chr1	10768635	10768762	E070	41615
chr1	10768980	10769042	E070	41960
chr1	10769113	10769213	E070	42093
chr1	10769418	10769563	E070	42398
chr1	10769615	10769728	E070	42595
chr1	10769817	10769931	E070	42797
chr1	10769960	10770084	E070	42940
chr1	10772662	10772802	E070	45642
chr1	10772825	10773470	E070	45805
chr1	10773551	10773602	E070	46531
chr1	10694645	10695194	E071	-31826
chr1	10695242	10696319	E071	-30701
chr1	10700718	10700866	E071	-26154
chr1	10700912	10701033	E071	-25987
chr1	10701085	10701135	E071	-25885
chr1	10723007	10723313	E071	-3707
chr1	10723387	10724295	E071	-2725
chr1	10725626	10725944	E071	-1076
chr1	10725989	10726476	E071	-544
chr1	10742209	10742367	E071	15189
chr1	10769817	10769931	E071	42797
chr1	10723007	10723313	E072	-3707
chr1	10723387	10724295	E072	-2725
chr1	10724441	10724697	E072	-2323
chr1	10725626	10725944	E072	-1076
chr1	10725989	10726476	E072	-544
chr1	10769615	10769728	E072	42595
chr1	10769817	10769931	E072	42797
chr1	10769960	10770084	E072	42940
chr1	10694645	10695194	E073	-31826
chr1	10723007	10723313	E073	-3707
chr1	10723387	10724295	E073	-2725
chr1	10723387	10724295	E074	-2725
chr1	10725626	10725944	E074	-1076
chr1	10725989	10726476	E074	-544
chr1	10726487	10726755	E074	-265
chr1	10695242	10696319	E081	-30701
chr1	10699890	10700675	E081	-26345
chr1	10700718	10700866	E081	-26154
chr1	10700912	10701033	E081	-25987
chr1	10711529	10711737	E081	-15283
chr1	10711855	10712174	E081	-14846
chr1	10722583	10722820	E081	-4200
chr1	10722892	10722989	E081	-4031
chr1	10723007	10723313	E081	-3707
chr1	10723387	10724295	E081	-2725
chr1	10724441	10724697	E081	-2323
chr1	10731201	10731514	E081	4181
chr1	10731564	10731686	E081	4544
chr1	10731720	10732119	E081	4700
chr1	10733491	10733680	E081	6471
chr1	10737231	10738061	E081	10211
chr1	10738134	10738259	E081	11114
chr1	10738329	10738466	E081	11309
chr1	10738761	10738860	E081	11741
chr1	10738967	10740291	E081	11947
chr1	10742209	10742367	E081	15189
chr1	10742504	10743011	E081	15484
chr1	10743017	10743352	E081	15997
chr1	10743354	10743692	E081	16334
chr1	10767551	10767643	E081	40531
chr1	10767773	10767886	E081	40753
chr1	10767907	10768047	E081	40887
chr1	10768182	10768272	E081	41162
chr1	10768635	10768762	E081	41615
chr1	10768980	10769042	E081	41960
chr1	10769113	10769213	E081	42093
chr1	10769418	10769563	E081	42398
chr1	10769615	10769728	E081	42595
chr1	10769817	10769931	E081	42797
chr1	10769960	10770084	E081	42940
chr1	10772662	10772802	E081	45642
chr1	10772825	10773470	E081	45805
chr1	10694645	10695194	E082	-31826
chr1	10695242	10696319	E082	-30701
chr1	10723387	10724295	E082	-2725
chr1	10724441	10724697	E082	-2323
chr1	10738134	10738259	E082	11114
chr1	10738329	10738466	E082	11309
chr1	10738761	10738860	E082	11741
chr1	10742504	10743011	E082	15484
chr1	10743776	10743895	E082	16756
chr1	10769113	10769213	E082	42093
chr1	10769418	10769563	E082	42398
chr1	10769615	10769728	E082	42595

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10753063	10755583	E067	26043
chr1	10753063	10755583	E068	26043
chr1	10755595	10755720	E068	28575
chr1	10753063	10755583	E069	26043
chr1	10755595	10755720	E069	28575
chr1	10698813	10698918	E070	-28102
chr1	10698970	10699106	E070	-27914
chr1	10699129	10699276	E070	-27744
chr1	10753063	10755583	E070	26043
chr1	10755595	10755720	E070	28575
chr1	10753063	10755583	E071	26043
chr1	10755595	10755720	E071	28575
chr1	10753063	10755583	E072	26043
chr1	10755595	10755720	E072	28575
chr1	10753063	10755583	E073	26043
chr1	10755595	10755720	E073	28575
chr1	10753063	10755583	E074	26043
chr1	10698304	10698417	E082	-28603
chr1	10698437	10698582	E082	-28438
chr1	10698617	10698657	E082	-28363
chr1	10698725	10698803	E082	-28217
chr1	10698813	10698918	E082	-28102
chr1	10698970	10699106	E082	-27914
chr1	10699129	10699276	E082	-27744
chr1	10753063	10755583	E082	26043
chr1	10755595	10755720	E082	28575