rs778228

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CASZ1 : Synonymous Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0336 (16094/47832,ExAC)
G=0290 (8643/29764,GnomAD)
G=0327 (9540/29118,TOPMED)
A==0267 (3450/12910,GO-ESP)
G=0329 (1649/5008,1000G)
G=0169 (652/3854,ALSPAC)
G=0189 (702/3708,TWINSUK)

Position: chr1:10648085 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 123 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.10648085A>G
GRCh37.p13 chr 1	NC_000001.10:g.10708142A>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....NM_001079843.2:c.3213T>C	F [TTT]> F [TTC]	Coding Sequence Variant
zinc finger protein castor homolog 1 isoform a	NP_001073312.1:p....NP_001073312.1:p.Phe1071=	F [Phe]> F [Phe]	Synonymous Variant
CASZ1 transcript variant 2	NM_017766.4:c.321...NM_017766.4:c.3213T>C	F [TTT]> F [TTC]	Coding Sequence Variant
zinc finger protein castor homolog 1 isoform b	NP_060236.3:p.Phe...NP_060236.3:p.Phe1071=	F [Phe]> F [Phe]	Synonymous Variant
CASZ1 transcript variant X1	XM_017001539.1:c....XM_017001539.1:c.3285T>C	F [TTT]> F [TTC]	Coding Sequence Variant
zinc finger protein castor homolog 1 isoform X1	XP_016857028.1:p....XP_016857028.1:p.Phe1095=	F [Phe]> F [Phe]	Synonymous Variant
CASZ1 transcript variant X2	XM_017001540.1:c....XM_017001540.1:c.3213T>C	F [TTT]> F [TTC]	Coding Sequence Variant
zinc finger protein castor homolog 1 isoform X2	XP_016857029.1:p....XP_016857029.1:p.Phe1071=	F [Phe]> F [Phe]	Synonymous Variant
CASZ1 transcript variant X3	XM_017001541.1:c....XM_017001541.1:c.3213T>C	F [TTT]> F [TTC]	Coding Sequence Variant
zinc finger protein castor homolog 1 isoform X2	XP_016857030.1:p....XP_016857030.1:p.Phe1071=	F [Phe]> F [Phe]	Synonymous Variant
CASZ1 transcript variant X4	XM_005263479.3:c....XM_005263479.3:c.3285T>C	F [TTT]> F [TTC]	Coding Sequence Variant
zinc finger protein castor homolog 1 isoform X3	XP_005263536.1:p....XP_005263536.1:p.Phe1095=	F [Phe]> F [Phe]	Synonymous Variant
CASZ1 transcript variant X5	XM_011541635.2:c....XM_011541635.2:c.3285T>C	F [TTT]> F [TTC]	Coding Sequence Variant
zinc finger protein castor homolog 1 isoform X4	XP_011539937.1:p....XP_011539937.1:p.Phe1095=	F [Phe]> F [Phe]	Synonymous Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.457	G=0.543
1000Genomes	American	Sub	694	A=0.810	G=0.190
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=0.671	G=0.329
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 Exome Aggregation Consortium	American	Sub	8558	A=0.557	G=0.443
The Exome Aggregation Consortium	Asian	Sub	11928	A=0.620	G=0.379
The Exome Aggregation Consortium	Europe	Sub	26996	A=0.716	G=0.284
The Exome Aggregation Consortium	Global	Study-wide	47832	A=0.663	G=0.336
The Exome Aggregation Consortium	Other	Sub	350	A=0.680	G=0.320
The Genome Aggregation Database	African	Sub	8664	A=0.520	G=0.480
The Genome Aggregation Database	American	Sub	836	A=0.810	G=0.190
The Genome Aggregation Database	East Asian	Sub	1612	A=0.749	G=0.251
The Genome Aggregation Database	Europe	Sub	18350	A=0.790	G=0.209
The Genome Aggregation Database	Global	Study-wide	29764	A=0.709	G=0.290
The Genome Aggregation Database	Other	Sub	302	A=0.760	G=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.672	G=0.327
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
27589061	Whole Exome Sequencing in Atrial Fibrillation.	Lubitz SA	PLoS Genet

P-Value

SNP ID	p-value	Traits	Study
rs778228	1.64E-06	alcohol dependence (age at onset)	24962325

eQTL of rs778228 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 rs778228 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg18878351	chr1:10709343	CASZ1	-0.0428125990478394	1.8326e-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	-33451
chr1	10676080	10676130	E067	-32012
chr1	10676190	10676279	E067	-31863
chr1	10723387	10724295	E067	15245
chr1	10725989	10726476	E067	17847
chr1	10674618	10674691	E068	-33451
chr1	10723387	10724295	E068	15245
chr1	10674618	10674691	E069	-33451
chr1	10676080	10676130	E069	-32012
chr1	10676190	10676279	E069	-31863
chr1	10723387	10724295	E069	15245
chr1	10725626	10725944	E069	17484
chr1	10725989	10726476	E069	17847
chr1	10755770	10755982	E069	47628
chr1	10658521	10658674	E070	-49468
chr1	10658819	10658900	E070	-49242
chr1	10659286	10659975	E070	-48167
chr1	10675435	10675632	E070	-32510
chr1	10676080	10676130	E070	-32012
chr1	10676190	10676279	E070	-31863
chr1	10676383	10676433	E070	-31709
chr1	10683745	10683802	E070	-24340
chr1	10692059	10692263	E070	-15879
chr1	10692491	10692700	E070	-15442
chr1	10692869	10693116	E070	-15026
chr1	10694645	10695194	E070	-12948
chr1	10695242	10696319	E070	-11823
chr1	10699890	10700675	E070	-7467
chr1	10700718	10700866	E070	-7276
chr1	10700912	10701033	E070	-7109
chr1	10701085	10701135	E070	-7007
chr1	10701359	10701479	E070	-6663
chr1	10708766	10708816	E070	624
chr1	10711529	10711737	E070	3387
chr1	10711855	10712174	E070	3713
chr1	10723007	10723313	E070	14865
chr1	10723387	10724295	E070	15245
chr1	10724441	10724697	E070	16299
chr1	10730791	10730871	E070	22649
chr1	10731201	10731514	E070	23059
chr1	10731564	10731686	E070	23422
chr1	10731720	10732119	E070	23578
chr1	10733491	10733680	E070	25349
chr1	10734074	10734134	E070	25932
chr1	10734771	10734824	E070	26629
chr1	10735138	10735403	E070	26996
chr1	10735523	10735640	E070	27381
chr1	10737231	10738061	E070	29089
chr1	10738134	10738259	E070	29992
chr1	10738329	10738466	E070	30187
chr1	10738761	10738860	E070	30619
chr1	10738967	10740291	E070	30825
chr1	10658521	10658674	E071	-49468
chr1	10674173	10674224	E071	-33918
chr1	10674618	10674691	E071	-33451
chr1	10675435	10675632	E071	-32510
chr1	10676080	10676130	E071	-32012
chr1	10676190	10676279	E071	-31863
chr1	10694645	10695194	E071	-12948
chr1	10695242	10696319	E071	-11823
chr1	10700718	10700866	E071	-7276
chr1	10700912	10701033	E071	-7109
chr1	10701085	10701135	E071	-7007
chr1	10723007	10723313	E071	14865
chr1	10723387	10724295	E071	15245
chr1	10725626	10725944	E071	17484
chr1	10725989	10726476	E071	17847
chr1	10742209	10742367	E071	34067
chr1	10674618	10674691	E072	-33451
chr1	10676080	10676130	E072	-32012
chr1	10676190	10676279	E072	-31863
chr1	10723007	10723313	E072	14865
chr1	10723387	10724295	E072	15245
chr1	10724441	10724697	E072	16299
chr1	10725626	10725944	E072	17484
chr1	10725989	10726476	E072	17847
chr1	10694645	10695194	E073	-12948
chr1	10723007	10723313	E073	14865
chr1	10723387	10724295	E073	15245
chr1	10674618	10674691	E074	-33451
chr1	10723387	10724295	E074	15245
chr1	10725626	10725944	E074	17484
chr1	10725989	10726476	E074	17847
chr1	10726487	10726755	E074	18345
chr1	10672536	10673120	E081	-35022
chr1	10675435	10675632	E081	-32510
chr1	10676080	10676130	E081	-32012
chr1	10676190	10676279	E081	-31863
chr1	10676383	10676433	E081	-31709
chr1	10695242	10696319	E081	-11823
chr1	10699890	10700675	E081	-7467
chr1	10700718	10700866	E081	-7276
chr1	10700912	10701033	E081	-7109
chr1	10711529	10711737	E081	3387
chr1	10711855	10712174	E081	3713
chr1	10722583	10722820	E081	14441
chr1	10722892	10722989	E081	14750
chr1	10723007	10723313	E081	14865
chr1	10723387	10724295	E081	15245
chr1	10724441	10724697	E081	16299
chr1	10731201	10731514	E081	23059
chr1	10731564	10731686	E081	23422
chr1	10731720	10732119	E081	23578
chr1	10733491	10733680	E081	25349
chr1	10737231	10738061	E081	29089
chr1	10738134	10738259	E081	29992
chr1	10738329	10738466	E081	30187
chr1	10738761	10738860	E081	30619
chr1	10738967	10740291	E081	30825
chr1	10742209	10742367	E081	34067
chr1	10742504	10743011	E081	34362
chr1	10743017	10743352	E081	34875
chr1	10743354	10743692	E081	35212
chr1	10675435	10675632	E082	-32510
chr1	10694645	10695194	E082	-12948
chr1	10695242	10696319	E082	-11823
chr1	10723387	10724295	E082	15245
chr1	10724441	10724697	E082	16299
chr1	10738134	10738259	E082	29992
chr1	10738329	10738466	E082	30187
chr1	10738761	10738860	E082	30619
chr1	10742504	10743011	E082	34362
chr1	10743776	10743895	E082	35634

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10753063	10755583	E067	44921
chr1	10753063	10755583	E068	44921
chr1	10755595	10755720	E068	47453
chr1	10753063	10755583	E069	44921
chr1	10755595	10755720	E069	47453
chr1	10698813	10698918	E070	-9224
chr1	10698970	10699106	E070	-9036
chr1	10699129	10699276	E070	-8866
chr1	10753063	10755583	E070	44921
chr1	10755595	10755720	E070	47453
chr1	10753063	10755583	E071	44921
chr1	10755595	10755720	E071	47453
chr1	10753063	10755583	E072	44921
chr1	10755595	10755720	E072	47453
chr1	10753063	10755583	E073	44921
chr1	10755595	10755720	E073	47453
chr1	10753063	10755583	E074	44921
chr1	10698304	10698417	E082	-9725
chr1	10698437	10698582	E082	-9560
chr1	10698617	10698657	E082	-9485
chr1	10698725	10698803	E082	-9339
chr1	10698813	10698918	E082	-9224
chr1	10698970	10699106	E082	-9036
chr1	10699129	10699276	E082	-8866
chr1	10753063	10755583	E082	44921
chr1	10755595	10755720	E082	47453