rs476164

Organism: Homo sapiens

Alleles: T>A / T>C

Gene : Feature

CASZ1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0242 (7244/29850,GnomAD)
C=0269 (7848/29118,TOPMED)
C=0241 (1205/5008,1000G)
C=0148 (572/3854,ALSPAC)
C=0158 (585/3708,TWINSUK)

Position: chr1:10659509 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 100 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.10659509T>A
GRCh38.p7 chr 1	NC_000001.11:g.10659509T>C
GRCh37.p13 chr 1	NC_000001.10:g.10719566T>A
GRCh37.p13 chr 1	NC_000001.10:g.10719566T>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=0.570	C=0.430
1000Genomes	American	Sub	694	T=0.830	C=0.170
1000Genomes	East Asian	Sub	1008	T=0.861	C=0.139
1000Genomes	Europe	Sub	1006	T=0.822	C=0.178
1000Genomes	Global	Study-wide	5008	T=0.759	C=0.241
1000Genomes	South Asian	Sub	978	T=0.790	C=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.852	C=0.148
The Genome Aggregation Database	African	Sub	8688	T=0.623	C=0.377
The Genome Aggregation Database	American	Sub	834	T=0.830	C=0.17,
The Genome Aggregation Database	East Asian	Sub	1616	T=0.830	C=0.170
The Genome Aggregation Database	Europe	Sub	18410	T=0.810	C=0.189
The Genome Aggregation Database	Global	Study-wide	29850	T=0.757	C=0.242
The Genome Aggregation Database	Other	Sub	302	T=0.770	C=0.23,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.730	C=0.269
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.842	C=0.158

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
rs476164	7.42E-06	alcohol dependence (age at onset)	24962325

eQTL of rs476164 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 rs476164 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

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	-4152
chr1	10676080	10676130	E067	-2713
chr1	10676190	10676279	E067	-2564
chr1	10723387	10724295	E067	44544
chr1	10725989	10726476	E067	47146
chr1	10658122	10658519	E068	-20324
chr1	10674618	10674691	E068	-4152
chr1	10723387	10724295	E068	44544
chr1	10674618	10674691	E069	-4152
chr1	10676080	10676130	E069	-2713
chr1	10676190	10676279	E069	-2564
chr1	10723387	10724295	E069	44544
chr1	10725626	10725944	E069	46783
chr1	10725989	10726476	E069	47146
chr1	10639682	10639816	E070	-39027
chr1	10657285	10657517	E070	-21326
chr1	10657636	10657777	E070	-21066
chr1	10657802	10657902	E070	-20941
chr1	10658122	10658519	E070	-20324
chr1	10658521	10658674	E070	-20169
chr1	10658819	10658900	E070	-19943
chr1	10659286	10659975	E070	-18868
chr1	10675435	10675632	E070	-3211
chr1	10676080	10676130	E070	-2713
chr1	10676190	10676279	E070	-2564
chr1	10676383	10676433	E070	-2410
chr1	10683745	10683802	E070	4902
chr1	10692059	10692263	E070	13216
chr1	10692491	10692700	E070	13648
chr1	10692869	10693116	E070	14026
chr1	10694645	10695194	E070	15802
chr1	10695242	10696319	E070	16399
chr1	10699890	10700675	E070	21047
chr1	10700718	10700866	E070	21875
chr1	10700912	10701033	E070	22069
chr1	10701085	10701135	E070	22242
chr1	10701359	10701479	E070	22516
chr1	10708766	10708816	E070	29923
chr1	10711529	10711737	E070	32686
chr1	10711855	10712174	E070	33012
chr1	10723007	10723313	E070	44164
chr1	10723387	10724295	E070	44544
chr1	10724441	10724697	E070	45598
chr1	10658122	10658519	E071	-20324
chr1	10658521	10658674	E071	-20169
chr1	10674173	10674224	E071	-4619
chr1	10674618	10674691	E071	-4152
chr1	10675435	10675632	E071	-3211
chr1	10676080	10676130	E071	-2713
chr1	10676190	10676279	E071	-2564
chr1	10694645	10695194	E071	15802
chr1	10695242	10696319	E071	16399
chr1	10700718	10700866	E071	21875
chr1	10700912	10701033	E071	22069
chr1	10701085	10701135	E071	22242
chr1	10723007	10723313	E071	44164
chr1	10723387	10724295	E071	44544
chr1	10725626	10725944	E071	46783
chr1	10725989	10726476	E071	47146
chr1	10658122	10658519	E072	-20324
chr1	10674618	10674691	E072	-4152
chr1	10676080	10676130	E072	-2713
chr1	10676190	10676279	E072	-2564
chr1	10723007	10723313	E072	44164
chr1	10723387	10724295	E072	44544
chr1	10724441	10724697	E072	45598
chr1	10725626	10725944	E072	46783
chr1	10725989	10726476	E072	47146
chr1	10658122	10658519	E073	-20324
chr1	10694645	10695194	E073	15802
chr1	10723007	10723313	E073	44164
chr1	10723387	10724295	E073	44544
chr1	10658122	10658519	E074	-20324
chr1	10674618	10674691	E074	-4152
chr1	10723387	10724295	E074	44544
chr1	10725626	10725944	E074	46783
chr1	10725989	10726476	E074	47146
chr1	10726487	10726755	E074	47644
chr1	10672536	10673120	E081	-5723
chr1	10675435	10675632	E081	-3211
chr1	10676080	10676130	E081	-2713
chr1	10676190	10676279	E081	-2564
chr1	10676383	10676433	E081	-2410
chr1	10695242	10696319	E081	16399
chr1	10699890	10700675	E081	21047
chr1	10700718	10700866	E081	21875
chr1	10700912	10701033	E081	22069
chr1	10711529	10711737	E081	32686
chr1	10711855	10712174	E081	33012
chr1	10722583	10722820	E081	43740
chr1	10722892	10722989	E081	44049
chr1	10723007	10723313	E081	44164
chr1	10723387	10724295	E081	44544
chr1	10724441	10724697	E081	45598
chr1	10652230	10652294	E082	-26549
chr1	10675435	10675632	E082	-3211
chr1	10694645	10695194	E082	15802
chr1	10695242	10696319	E082	16399
chr1	10723387	10724295	E082	44544
chr1	10724441	10724697	E082	45598

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	19970
chr1	10698970	10699106	E070	20127
chr1	10699129	10699276	E070	20286
chr1	10698304	10698417	E082	19461
chr1	10698437	10698582	E082	19594
chr1	10698617	10698657	E082	19774
chr1	10698725	10698803	E082	19882
chr1	10698813	10698918	E082	19970
chr1	10698970	10699106	E082	20127
chr1	10699129	10699276	E082	20286