rs3790598

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

CAPZA1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0115 (3447/29918,GnomAD)
A=0089 (446/5008,1000G)

Position: chr1:112654274 (GRCh38.p7) (1p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 283 Enhancers around

Promoter: 8 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.112654274G>A
GRCh38.p7 chr 1	NC_000001.11:g.112654274G>T
GRCh37.p13 chr 1	NC_000001.10:g.113196896G>A
GRCh37.p13 chr 1	NC_000001.10:g.113196896G>T

Gene: CAPZA1, capping actin protein of muscle Z-line alpha subunit 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CAPZA1 transcript	NM_006135.2:c.	N/A	Intron Variant
CAPZA1 transcript variant X2	XM_011542225.2:c.	N/A	Intron Variant
CAPZA1 transcript variant X1	XM_017002424.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.993	A=0.007
1000Genomes	American	Sub	694	G=0.920	A=0.080
1000Genomes	East Asian	Sub	1008	G=0.931	A=0.069
1000Genomes	Europe	Sub	1006	G=0.826	A=0.174
1000Genomes	Global	Study-wide	5008	G=0.911	A=0.089
1000Genomes	South Asian	Sub	978	G=0.860	A=0.140
The Genome Aggregation Database	African	Sub	8718	G=0.967	A=0.033
The Genome Aggregation Database	American	Sub	836	G=0.900	A=0.09,
The Genome Aggregation Database	East Asian	Sub	1614	G=0.928	A=0.072
The Genome Aggregation Database	Europe	Sub	18448	G=0.843	A=0.156
The Genome Aggregation Database	Global	Study-wide	29918	G=0.884	A=0.115
The Genome Aggregation Database	Other	Sub	302	G=0.750	A=0.25,

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs3790598	0.000191	alcohol dependence	20201924

eQTL of rs3790598 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:113196896	WNT2B	ENSG00000134245.13	G>A	1.0612e-8	187733	Frontal_Cortex_BA9
Chr1:113196896	WNT2B	ENSG00000134245.13	G>A	1.3176e-10	187733	Cortex

meQTL of rs3790598 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	25785196	25785297	E067	-49671
chr1	25785301	25785693	E067	-49275
chr1	25786646	25786723	E067	-48245
chr1	25788374	25788824	E067	-46144
chr1	25788865	25788915	E067	-46053
chr1	25789022	25789080	E067	-45888
chr1	25789325	25789485	E067	-45483
chr1	25807665	25807836	E067	-27132
chr1	25808261	25808387	E067	-26581
chr1	25808504	25808630	E067	-26338
chr1	25810679	25810845	E067	-24123
chr1	25810925	25810983	E067	-23985
chr1	25811165	25811218	E067	-23750
chr1	25868876	25869047	E067	33908
chr1	25871941	25872058	E067	36973
chr1	25872107	25872160	E067	37139
chr1	25872162	25872206	E067	37194
chr1	25872820	25872874	E067	37852
chr1	25875728	25875887	E067	40760
chr1	25875913	25876642	E067	40945
chr1	25876676	25876916	E067	41708
chr1	25877084	25877215	E067	42116
chr1	25877271	25877479	E067	42303
chr1	25878200	25878258	E067	43232
chr1	25878388	25878428	E067	43420
chr1	25879038	25879177	E067	44070
chr1	25879552	25879601	E067	44584
chr1	25879643	25879726	E067	44675
chr1	25880698	25880902	E067	45730
chr1	25881035	25881079	E067	46067
chr1	25881649	25881884	E067	46681
chr1	25882034	25882074	E067	47066
chr1	25882108	25882163	E067	47140
chr1	25882223	25882301	E067	47255
chr1	25882572	25882674	E067	47604
chr1	25882975	25883070	E067	48007
chr1	25883124	25883677	E067	48156
chr1	25884191	25884326	E067	49223
chr1	25788374	25788824	E068	-46144
chr1	25800548	25800589	E068	-34379
chr1	25802741	25803198	E068	-31770
chr1	25808261	25808387	E068	-26581
chr1	25810679	25810845	E068	-24123
chr1	25810925	25810983	E068	-23985
chr1	25848908	25849031	E068	13940
chr1	25849101	25849155	E068	14133
chr1	25851236	25851286	E068	16268
chr1	25871941	25872058	E068	36973
chr1	25872107	25872160	E068	37139
chr1	25872162	25872206	E068	37194
chr1	25872531	25872609	E068	37563
chr1	25872686	25872740	E068	37718
chr1	25872820	25872874	E068	37852
chr1	25872900	25873012	E068	37932
chr1	25875395	25875515	E068	40427
chr1	25875728	25875887	E068	40760
chr1	25875913	25876642	E068	40945
chr1	25876676	25876916	E068	41708
chr1	25877084	25877215	E068	42116
chr1	25877271	25877479	E068	42303
chr1	25878388	25878428	E068	43420
chr1	25879038	25879177	E068	44070
chr1	25882975	25883070	E068	48007
chr1	25883124	25883677	E068	48156
chr1	25884191	25884326	E068	49223
chr1	25788865	25788915	E069	-46053
chr1	25789022	25789080	E069	-45888
chr1	25789325	25789485	E069	-45483
chr1	25793776	25793931	E069	-41037
chr1	25793984	25794059	E069	-40909
chr1	25794264	25794464	E069	-40504
chr1	25794609	25794844	E069	-40124
chr1	25800290	25800358	E069	-34610
chr1	25800548	25800589	E069	-34379
chr1	25802741	25803198	E069	-31770
chr1	25871941	25872058	E069	36973
chr1	25872107	25872160	E069	37139
chr1	25872162	25872206	E069	37194
chr1	25872531	25872609	E069	37563
chr1	25874568	25874711	E069	39600
chr1	25875395	25875515	E069	40427
chr1	25875728	25875887	E069	40760
chr1	25875913	25876642	E069	40945
chr1	25876676	25876916	E069	41708
chr1	25877084	25877215	E069	42116
chr1	25877271	25877479	E069	42303
chr1	25878200	25878258	E069	43232
chr1	25878388	25878428	E069	43420
chr1	25879038	25879177	E069	44070
chr1	25879552	25879601	E069	44584
chr1	25879643	25879726	E069	44675
chr1	25879824	25879872	E069	44856
chr1	25879914	25879984	E069	44946
chr1	25880698	25880902	E069	45730
chr1	25881035	25881079	E069	46067
chr1	25881649	25881884	E069	46681
chr1	25882034	25882074	E069	47066
chr1	25882108	25882163	E069	47140
chr1	25882223	25882301	E069	47255
chr1	25882975	25883070	E069	48007
chr1	25883124	25883677	E069	48156
chr1	25884191	25884326	E069	49223
chr1	25788865	25788915	E070	-46053
chr1	25786646	25786723	E071	-48245
chr1	25789325	25789485	E071	-45483
chr1	25793776	25793931	E071	-41037
chr1	25793984	25794059	E071	-40909
chr1	25794264	25794464	E071	-40504
chr1	25794609	25794844	E071	-40124
chr1	25794901	25794988	E071	-39980
chr1	25795110	25795218	E071	-39750
chr1	25795331	25795439	E071	-39529
chr1	25807665	25807836	E071	-27132
chr1	25812149	25812310	E071	-22658
chr1	25812344	25812394	E071	-22574
chr1	25813222	25813407	E071	-21561
chr1	25831444	25831580	E071	-3388
chr1	25863509	25863563	E071	28541
chr1	25863580	25863794	E071	28612
chr1	25863848	25863971	E071	28880
chr1	25863979	25864029	E071	29011
chr1	25868424	25868767	E071	33456
chr1	25868876	25869047	E071	33908
chr1	25871941	25872058	E071	36973
chr1	25872107	25872160	E071	37139
chr1	25872162	25872206	E071	37194
chr1	25872531	25872609	E071	37563
chr1	25872686	25872740	E071	37718
chr1	25872820	25872874	E071	37852
chr1	25872900	25873012	E071	37932
chr1	25874568	25874711	E071	39600
chr1	25875395	25875515	E071	40427
chr1	25875728	25875887	E071	40760
chr1	25875913	25876642	E071	40945
chr1	25876676	25876916	E071	41708
chr1	25877084	25877215	E071	42116
chr1	25877271	25877479	E071	42303
chr1	25878200	25878258	E071	43232
chr1	25878388	25878428	E071	43420
chr1	25879038	25879177	E071	44070
chr1	25879552	25879601	E071	44584
chr1	25879643	25879726	E071	44675
chr1	25879824	25879872	E071	44856
chr1	25879914	25879984	E071	44946
chr1	25880698	25880902	E071	45730
chr1	25881035	25881079	E071	46067
chr1	25881649	25881884	E071	46681
chr1	25882034	25882074	E071	47066
chr1	25882108	25882163	E071	47140
chr1	25882223	25882301	E071	47255
chr1	25882572	25882674	E071	47604
chr1	25882975	25883070	E071	48007
chr1	25883124	25883677	E071	48156
chr1	25884191	25884326	E071	49223
chr1	25788374	25788824	E072	-46144
chr1	25788865	25788915	E072	-46053
chr1	25789022	25789080	E072	-45888
chr1	25794609	25794844	E072	-40124
chr1	25794901	25794988	E072	-39980
chr1	25802741	25803198	E072	-31770
chr1	25807665	25807836	E072	-27132
chr1	25810679	25810845	E072	-24123
chr1	25813222	25813407	E072	-21561
chr1	25847040	25847391	E072	12072
chr1	25847396	25847577	E072	12428
chr1	25868424	25868767	E072	33456
chr1	25868876	25869047	E072	33908
chr1	25871941	25872058	E072	36973
chr1	25872107	25872160	E072	37139
chr1	25872162	25872206	E072	37194
chr1	25872531	25872609	E072	37563
chr1	25872686	25872740	E072	37718
chr1	25872820	25872874	E072	37852
chr1	25872900	25873012	E072	37932
chr1	25875395	25875515	E072	40427
chr1	25875728	25875887	E072	40760
chr1	25875913	25876642	E072	40945
chr1	25876676	25876916	E072	41708
chr1	25877084	25877215	E072	42116
chr1	25877271	25877479	E072	42303
chr1	25878200	25878258	E072	43232
chr1	25878388	25878428	E072	43420
chr1	25879038	25879177	E072	44070
chr1	25879552	25879601	E072	44584
chr1	25879643	25879726	E072	44675
chr1	25879824	25879872	E072	44856
chr1	25879914	25879984	E072	44946
chr1	25880698	25880902	E072	45730
chr1	25881649	25881884	E072	46681
chr1	25882034	25882074	E072	47066
chr1	25882108	25882163	E072	47140
chr1	25882223	25882301	E072	47255
chr1	25882572	25882674	E072	47604
chr1	25882975	25883070	E072	48007
chr1	25883124	25883677	E072	48156
chr1	25884191	25884326	E072	49223
chr1	25786646	25786723	E073	-48245
chr1	25788374	25788824	E073	-46144
chr1	25788865	25788915	E073	-46053
chr1	25789022	25789080	E073	-45888
chr1	25789325	25789485	E073	-45483
chr1	25794609	25794844	E073	-40124
chr1	25794901	25794988	E073	-39980
chr1	25810679	25810845	E073	-24123
chr1	25811165	25811218	E073	-23750
chr1	25811393	25811469	E073	-23499
chr1	25831678	25831791	E073	-3177
chr1	25848908	25849031	E073	13940
chr1	25849101	25849155	E073	14133
chr1	25851236	25851286	E073	16268
chr1	25868876	25869047	E073	33908
chr1	25871941	25872058	E073	36973
chr1	25872107	25872160	E073	37139
chr1	25872162	25872206	E073	37194
chr1	25875728	25875887	E073	40760
chr1	25875913	25876642	E073	40945
chr1	25876676	25876916	E073	41708
chr1	25877084	25877215	E073	42116
chr1	25877271	25877479	E073	42303
chr1	25878388	25878428	E073	43420
chr1	25879038	25879177	E073	44070
chr1	25879552	25879601	E073	44584
chr1	25879643	25879726	E073	44675
chr1	25882572	25882674	E073	47604
chr1	25882975	25883070	E073	48007
chr1	25883124	25883677	E073	48156
chr1	25788865	25788915	E074	-46053
chr1	25789022	25789080	E074	-45888
chr1	25789325	25789485	E074	-45483
chr1	25793776	25793931	E074	-41037
chr1	25793984	25794059	E074	-40909
chr1	25808261	25808387	E074	-26581
chr1	25808504	25808630	E074	-26338
chr1	25868876	25869047	E074	33908
chr1	25871941	25872058	E074	36973
chr1	25872107	25872160	E074	37139
chr1	25872162	25872206	E074	37194
chr1	25872531	25872609	E074	37563
chr1	25872686	25872740	E074	37718
chr1	25872820	25872874	E074	37852
chr1	25872900	25873012	E074	37932
chr1	25874568	25874711	E074	39600
chr1	25875395	25875515	E074	40427
chr1	25875728	25875887	E074	40760
chr1	25875913	25876642	E074	40945
chr1	25876676	25876916	E074	41708
chr1	25877084	25877215	E074	42116
chr1	25877271	25877479	E074	42303
chr1	25878200	25878258	E074	43232
chr1	25878388	25878428	E074	43420
chr1	25879038	25879177	E074	44070
chr1	25879552	25879601	E074	44584
chr1	25879643	25879726	E074	44675
chr1	25879824	25879872	E074	44856
chr1	25879914	25879984	E074	44946
chr1	25880698	25880902	E074	45730
chr1	25881035	25881079	E074	46067
chr1	25881649	25881884	E074	46681
chr1	25882572	25882674	E074	47604
chr1	25882975	25883070	E074	48007
chr1	25883124	25883677	E074	48156
chr1	25884191	25884326	E074	49223
chr1	25788374	25788824	E081	-46144
chr1	25788865	25788915	E081	-46053
chr1	25789022	25789080	E081	-45888
chr1	25789325	25789485	E081	-45483
chr1	25791927	25792130	E081	-42838
chr1	25793984	25794059	E081	-40909
chr1	25794264	25794464	E081	-40504
chr1	25794609	25794844	E081	-40124
chr1	25794901	25794988	E081	-39980
chr1	25807665	25807836	E081	-27132
chr1	25853341	25854170	E081	18373
chr1	25854182	25854306	E081	19214
chr1	25854617	25854667	E081	19649
chr1	25855260	25855334	E081	20292
chr1	25867941	25868129	E081	32973
chr1	25871941	25872058	E081	36973
chr1	25872107	25872160	E081	37139
chr1	25872162	25872206	E081	37194
chr1	25788374	25788824	E082	-46144
chr1	25854182	25854306	E082	19214
chr1	25854617	25854667	E082	19649

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	25869603	25871808	E067	34635
chr1	25869603	25871808	E068	34635
chr1	25869603	25871808	E069	34635
chr1	25869603	25871808	E071	34635
chr1	25869603	25871808	E072	34635
chr1	25869603	25871808	E073	34635
chr1	25869603	25871808	E074	34635
chr1	25869603	25871808	E082	34635