rs2242287

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CASZ1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0194 (5802/29914,GnomAD)
C=0191 (5585/29118,TOPMED)
C=0187 (935/5008,1000G)
C=0149 (575/3854,ALSPAC)
C=0158 (585/3708,TWINSUK)

Position: chr1:10654854 (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.10654854T>C
GRCh37.p13 chr 1	NC_000001.10:g.10714911T>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=0.765	C=0.235
1000Genomes	American	Sub	694	T=0.850	C=0.150
1000Genomes	East Asian	Sub	1008	T=0.863	C=0.137
1000Genomes	Europe	Sub	1006	T=0.821	C=0.179
1000Genomes	Global	Study-wide	5008	T=0.813	C=0.187
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=0.851	C=0.149
The Genome Aggregation Database	African	Sub	8708	T=0.790	C=0.210
The Genome Aggregation Database	American	Sub	836	T=0.840	C=0.160
The Genome Aggregation Database	East Asian	Sub	1620	T=0.828	C=0.172
The Genome Aggregation Database	Europe	Sub	18448	T=0.811	C=0.188
The Genome Aggregation Database	Global	Study-wide	29914	T=0.806	C=0.194
The Genome Aggregation Database	Other	Sub	302	T=0.770	C=0.230
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.808	C=0.191
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
rs2242287	6.42E-06	alcohol dependence (age at onset)	24962325

eQTL of rs2242287 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 rs2242287 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	-40220
chr1	10676080	10676130	E067	-38781
chr1	10676190	10676279	E067	-38632
chr1	10723387	10724295	E067	8476
chr1	10725989	10726476	E067	11078
chr1	10674618	10674691	E068	-40220
chr1	10723387	10724295	E068	8476
chr1	10674618	10674691	E069	-40220
chr1	10676080	10676130	E069	-38781
chr1	10676190	10676279	E069	-38632
chr1	10723387	10724295	E069	8476
chr1	10725626	10725944	E069	10715
chr1	10725989	10726476	E069	11078
chr1	10755770	10755982	E069	40859
chr1	10675435	10675632	E070	-39279
chr1	10676080	10676130	E070	-38781
chr1	10676190	10676279	E070	-38632
chr1	10676383	10676433	E070	-38478
chr1	10683745	10683802	E070	-31109
chr1	10692059	10692263	E070	-22648
chr1	10692491	10692700	E070	-22211
chr1	10692869	10693116	E070	-21795
chr1	10694645	10695194	E070	-19717
chr1	10695242	10696319	E070	-18592
chr1	10699890	10700675	E070	-14236
chr1	10700718	10700866	E070	-14045
chr1	10700912	10701033	E070	-13878
chr1	10701085	10701135	E070	-13776
chr1	10701359	10701479	E070	-13432
chr1	10708766	10708816	E070	-6095
chr1	10711529	10711737	E070	-3174
chr1	10711855	10712174	E070	-2737
chr1	10723007	10723313	E070	8096
chr1	10723387	10724295	E070	8476
chr1	10724441	10724697	E070	9530
chr1	10730791	10730871	E070	15880
chr1	10731201	10731514	E070	16290
chr1	10731564	10731686	E070	16653
chr1	10731720	10732119	E070	16809
chr1	10733491	10733680	E070	18580
chr1	10734074	10734134	E070	19163
chr1	10734771	10734824	E070	19860
chr1	10735138	10735403	E070	20227
chr1	10735523	10735640	E070	20612
chr1	10737231	10738061	E070	22320
chr1	10738134	10738259	E070	23223
chr1	10738329	10738466	E070	23418
chr1	10738761	10738860	E070	23850
chr1	10738967	10740291	E070	24056
chr1	10674173	10674224	E071	-40687
chr1	10674618	10674691	E071	-40220
chr1	10675435	10675632	E071	-39279
chr1	10676080	10676130	E071	-38781
chr1	10676190	10676279	E071	-38632
chr1	10694645	10695194	E071	-19717
chr1	10695242	10696319	E071	-18592
chr1	10700718	10700866	E071	-14045
chr1	10700912	10701033	E071	-13878
chr1	10701085	10701135	E071	-13776
chr1	10723007	10723313	E071	8096
chr1	10723387	10724295	E071	8476
chr1	10725626	10725944	E071	10715
chr1	10725989	10726476	E071	11078
chr1	10742209	10742367	E071	27298
chr1	10674618	10674691	E072	-40220
chr1	10676080	10676130	E072	-38781
chr1	10676190	10676279	E072	-38632
chr1	10723007	10723313	E072	8096
chr1	10723387	10724295	E072	8476
chr1	10724441	10724697	E072	9530
chr1	10725626	10725944	E072	10715
chr1	10725989	10726476	E072	11078
chr1	10694645	10695194	E073	-19717
chr1	10723007	10723313	E073	8096
chr1	10723387	10724295	E073	8476
chr1	10674618	10674691	E074	-40220
chr1	10723387	10724295	E074	8476
chr1	10725626	10725944	E074	10715
chr1	10725989	10726476	E074	11078
chr1	10726487	10726755	E074	11576
chr1	10672536	10673120	E081	-41791
chr1	10675435	10675632	E081	-39279
chr1	10676080	10676130	E081	-38781
chr1	10676190	10676279	E081	-38632
chr1	10676383	10676433	E081	-38478
chr1	10695242	10696319	E081	-18592
chr1	10699890	10700675	E081	-14236
chr1	10700718	10700866	E081	-14045
chr1	10700912	10701033	E081	-13878
chr1	10711529	10711737	E081	-3174
chr1	10711855	10712174	E081	-2737
chr1	10722583	10722820	E081	7672
chr1	10722892	10722989	E081	7981
chr1	10723007	10723313	E081	8096
chr1	10723387	10724295	E081	8476
chr1	10724441	10724697	E081	9530
chr1	10731201	10731514	E081	16290
chr1	10731564	10731686	E081	16653
chr1	10731720	10732119	E081	16809
chr1	10733491	10733680	E081	18580
chr1	10737231	10738061	E081	22320
chr1	10738134	10738259	E081	23223
chr1	10738329	10738466	E081	23418
chr1	10738761	10738860	E081	23850
chr1	10738967	10740291	E081	24056
chr1	10742209	10742367	E081	27298
chr1	10742504	10743011	E081	27593
chr1	10743017	10743352	E081	28106
chr1	10743354	10743692	E081	28443
chr1	10675435	10675632	E082	-39279
chr1	10694645	10695194	E082	-19717
chr1	10695242	10696319	E082	-18592
chr1	10723387	10724295	E082	8476
chr1	10724441	10724697	E082	9530
chr1	10738134	10738259	E082	23223
chr1	10738329	10738466	E082	23418
chr1	10738761	10738860	E082	23850
chr1	10742504	10743011	E082	27593
chr1	10743776	10743895	E082	28865

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10753063	10755583	E067	38152
chr1	10753063	10755583	E068	38152
chr1	10755595	10755720	E068	40684
chr1	10753063	10755583	E069	38152
chr1	10755595	10755720	E069	40684
chr1	10698813	10698918	E070	-15993
chr1	10698970	10699106	E070	-15805
chr1	10699129	10699276	E070	-15635
chr1	10753063	10755583	E070	38152
chr1	10755595	10755720	E070	40684
chr1	10753063	10755583	E071	38152
chr1	10755595	10755720	E071	40684
chr1	10753063	10755583	E072	38152
chr1	10755595	10755720	E072	40684
chr1	10753063	10755583	E073	38152
chr1	10755595	10755720	E073	40684
chr1	10753063	10755583	E074	38152
chr1	10698304	10698417	E082	-16494
chr1	10698437	10698582	E082	-16329
chr1	10698617	10698657	E082	-16254
chr1	10698725	10698803	E082	-16108
chr1	10698813	10698918	E082	-15993
chr1	10698970	10699106	E082	-15805
chr1	10699129	10699276	E082	-15635
chr1	10753063	10755583	E082	38152
chr1	10755595	10755720	E082	40684