rs1933932

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

ATPAF1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0079 (2396/29980,GnomAD)
C==0098 (2881/29118,TOPMED)
C==0186 (931/5008,1000G)
C==0003 (12/3854,ALSPAC)
C==0002 (9/3708,TWINSUK)

Position: chr1:46643656 (GRCh38.p7) (1p33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 167 Enhancers around

Promoter: 45 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.46643656C>T
GRCh37.p13 chr 1	NC_000001.10:g.47109328C>T

Gene: ATPAF1, ATP synthase mitochondrial F1 complex assembly factor 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATPAF1 transcript variant 2	NM_001042546.2:c.	N/A	Intron Variant
ATPAF1 transcript variant 3	NM_001243728.1:c.	N/A	Intron Variant
ATPAF1 transcript variant 4	NM_001256418.1:c.	N/A	Intron Variant
ATPAF1 transcript variant 1	NM_022745.4:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.238	T=0.762
1000Genomes	American	Sub	694	C=0.050	T=0.950
1000Genomes	East Asian	Sub	1008	C=0.425	T=0.575
1000Genomes	Europe	Sub	1006	C=0.013	T=0.987
1000Genomes	Global	Study-wide	5008	C=0.186	T=0.814
1000Genomes	South Asian	Sub	978	C=0.150	T=0.850
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.003	T=0.997
The Genome Aggregation Database	African	Sub	8716	C=0.175	T=0.825
The Genome Aggregation Database	American	Sub	838	C=0.050	T=0.950
The Genome Aggregation Database	East Asian	Sub	1614	C=0.395	T=0.605
The Genome Aggregation Database	Europe	Sub	18510	C=0.010	T=0.989
The Genome Aggregation Database	Global	Study-wide	29980	C=0.079	T=0.920
The Genome Aggregation Database	Other	Sub	302	C=0.010	T=0.990
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.098	T=0.901
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.002	T=0.998

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs1933932	0.00089	alcohol dependence	21314694

eQTL of rs1933932 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 rs1933932 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	47064426	47064526	E067	-44802
chr1	47065140	47065774	E067	-43554
chr1	47065807	47066011	E067	-43317
chr1	47068642	47068696	E067	-40632
chr1	47070790	47070885	E067	-38443
chr1	47078714	47079948	E067	-29380
chr1	47080027	47080155	E067	-29173
chr1	47080197	47080377	E067	-28951
chr1	47080472	47080565	E067	-28763
chr1	47081011	47081061	E067	-28267
chr1	47108990	47109458	E067	0
chr1	47131862	47131977	E067	22534
chr1	47153688	47154030	E067	44360
chr1	47156942	47157092	E067	47614
chr1	47157752	47157847	E067	48424
chr1	47157930	47158026	E067	48602
chr1	47158051	47158111	E067	48723
chr1	47158152	47158204	E067	48824
chr1	47060925	47061168	E068	-48160
chr1	47061218	47061292	E068	-48036
chr1	47061357	47061463	E068	-47865
chr1	47065140	47065774	E068	-43554
chr1	47068642	47068696	E068	-40632
chr1	47073722	47073785	E068	-35543
chr1	47077443	47077905	E068	-31423
chr1	47078714	47079948	E068	-29380
chr1	47080027	47080155	E068	-29173
chr1	47080197	47080377	E068	-28951
chr1	47080472	47080565	E068	-28763
chr1	47080667	47080760	E068	-28568
chr1	47080824	47080887	E068	-28441
chr1	47108990	47109458	E068	0
chr1	47131862	47131977	E068	22534
chr1	47153688	47154030	E068	44360
chr1	47157752	47157847	E068	48424
chr1	47157930	47158026	E068	48602
chr1	47158051	47158111	E068	48723
chr1	47158152	47158204	E068	48824
chr1	47158205	47158293	E068	48877
chr1	47158605	47158745	E068	49277
chr1	47065140	47065774	E069	-43554
chr1	47065807	47066011	E069	-43317
chr1	47067008	47067250	E069	-42078
chr1	47073102	47073397	E069	-35931
chr1	47073496	47073653	E069	-35675
chr1	47073722	47073785	E069	-35543
chr1	47078714	47079948	E069	-29380
chr1	47080027	47080155	E069	-29173
chr1	47080197	47080377	E069	-28951
chr1	47080472	47080565	E069	-28763
chr1	47080667	47080760	E069	-28568
chr1	47080824	47080887	E069	-28441
chr1	47089526	47089638	E069	-19690
chr1	47089780	47089929	E069	-19399
chr1	47089937	47090275	E069	-19053
chr1	47108990	47109458	E069	0
chr1	47131862	47131977	E069	22534
chr1	47153688	47154030	E069	44360
chr1	47156942	47157092	E069	47614
chr1	47157752	47157847	E069	48424
chr1	47157930	47158026	E069	48602
chr1	47158051	47158111	E069	48723
chr1	47158152	47158204	E069	48824
chr1	47064426	47064526	E070	-44802
chr1	47068642	47068696	E070	-40632
chr1	47078714	47079948	E070	-29380
chr1	47107844	47108044	E070	-1284
chr1	47108990	47109458	E070	0
chr1	47060662	47060799	E071	-48529
chr1	47060925	47061168	E071	-48160
chr1	47061218	47061292	E071	-48036
chr1	47061357	47061463	E071	-47865
chr1	47065140	47065774	E071	-43554
chr1	47065807	47066011	E071	-43317
chr1	47073496	47073653	E071	-35675
chr1	47073722	47073785	E071	-35543
chr1	47076829	47076936	E071	-32392
chr1	47077443	47077905	E071	-31423
chr1	47080197	47080377	E071	-28951
chr1	47080472	47080565	E071	-28763
chr1	47080667	47080760	E071	-28568
chr1	47089526	47089638	E071	-19690
chr1	47089780	47089929	E071	-19399
chr1	47089937	47090275	E071	-19053
chr1	47108990	47109458	E071	0
chr1	47131862	47131977	E071	22534
chr1	47152164	47152246	E071	42836
chr1	47152384	47152482	E071	43056
chr1	47152763	47152822	E071	43435
chr1	47153044	47153262	E071	43716
chr1	47153688	47154030	E071	44360
chr1	47154052	47154109	E071	44724
chr1	47154166	47154266	E071	44838
chr1	47156942	47157092	E071	47614
chr1	47157752	47157847	E071	48424
chr1	47157930	47158026	E071	48602
chr1	47158051	47158111	E071	48723
chr1	47158152	47158204	E071	48824
chr1	47158205	47158293	E071	48877
chr1	47158605	47158745	E071	49277
chr1	47060925	47061168	E072	-48160
chr1	47065140	47065774	E072	-43554
chr1	47065807	47066011	E072	-43317
chr1	47067008	47067250	E072	-42078
chr1	47073102	47073397	E072	-35931
chr1	47073496	47073653	E072	-35675
chr1	47073722	47073785	E072	-35543
chr1	47078714	47079948	E072	-29380
chr1	47080027	47080155	E072	-29173
chr1	47080197	47080377	E072	-28951
chr1	47080824	47080887	E072	-28441
chr1	47081011	47081061	E072	-28267
chr1	47089526	47089638	E072	-19690
chr1	47089780	47089929	E072	-19399
chr1	47108990	47109458	E072	0
chr1	47131862	47131977	E072	22534
chr1	47153688	47154030	E072	44360
chr1	47156942	47157092	E072	47614
chr1	47157752	47157847	E072	48424
chr1	47157930	47158026	E072	48602
chr1	47158051	47158111	E072	48723
chr1	47158152	47158204	E072	48824
chr1	47158205	47158293	E072	48877
chr1	47158605	47158745	E072	49277
chr1	47067008	47067250	E073	-42078
chr1	47068090	47068130	E073	-41198
chr1	47068135	47068242	E073	-41086
chr1	47068272	47068316	E073	-41012
chr1	47073496	47073653	E073	-35675
chr1	47073722	47073785	E073	-35543
chr1	47078714	47079948	E073	-29380
chr1	47080027	47080155	E073	-29173
chr1	47080197	47080377	E073	-28951
chr1	47080472	47080565	E073	-28763
chr1	47080667	47080760	E073	-28568
chr1	47080824	47080887	E073	-28441
chr1	47081011	47081061	E073	-28267
chr1	47108990	47109458	E073	0
chr1	47131862	47131977	E073	22534
chr1	47156942	47157092	E073	47614
chr1	47157752	47157847	E073	48424
chr1	47157930	47158026	E073	48602
chr1	47065140	47065774	E074	-43554
chr1	47073496	47073653	E074	-35675
chr1	47073722	47073785	E074	-35543
chr1	47077443	47077905	E074	-31423
chr1	47078714	47079948	E074	-29380
chr1	47080197	47080377	E074	-28951
chr1	47080472	47080565	E074	-28763
chr1	47080667	47080760	E074	-28568
chr1	47080824	47080887	E074	-28441
chr1	47081011	47081061	E074	-28267
chr1	47108990	47109458	E074	0
chr1	47131862	47131977	E074	22534
chr1	47153688	47154030	E074	44360
chr1	47154052	47154109	E074	44724
chr1	47154166	47154266	E074	44838
chr1	47156942	47157092	E074	47614
chr1	47068642	47068696	E081	-40632
chr1	47089937	47090275	E081	-19053
chr1	47108990	47109458	E081	0
chr1	47153044	47153262	E081	43716
chr1	47153688	47154030	E081	44360
chr1	47154052	47154109	E081	44724
chr1	47154166	47154266	E081	44838
chr1	47068642	47068696	E082	-40632
chr1	47153044	47153262	E082	43716

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	47069136	47070318	E067	-39010
chr1	47081782	47083126	E067	-26202
chr1	47133179	47134552	E067	23851
chr1	47134569	47134666	E067	25241
chr1	47134734	47134895	E067	25406
chr1	47069136	47070318	E068	-39010
chr1	47081782	47083126	E068	-26202
chr1	47133179	47134552	E068	23851
chr1	47134569	47134666	E068	25241
chr1	47134734	47134895	E068	25406
chr1	47069136	47070318	E069	-39010
chr1	47081782	47083126	E069	-26202
chr1	47133179	47134552	E069	23851
chr1	47134569	47134666	E069	25241
chr1	47134734	47134895	E069	25406
chr1	47069136	47070318	E070	-39010
chr1	47081782	47083126	E070	-26202
chr1	47133179	47134552	E070	23851
chr1	47069136	47070318	E071	-39010
chr1	47081782	47083126	E071	-26202
chr1	47133179	47134552	E071	23851
chr1	47134569	47134666	E071	25241
chr1	47134734	47134895	E071	25406
chr1	47069136	47070318	E072	-39010
chr1	47081782	47083126	E072	-26202
chr1	47133179	47134552	E072	23851
chr1	47134569	47134666	E072	25241
chr1	47069136	47070318	E073	-39010
chr1	47081782	47083126	E073	-26202
chr1	47133179	47134552	E073	23851
chr1	47134569	47134666	E073	25241
chr1	47134734	47134895	E073	25406
chr1	47069136	47070318	E074	-39010
chr1	47081782	47083126	E074	-26202
chr1	47133179	47134552	E074	23851
chr1	47134569	47134666	E074	25241
chr1	47134734	47134895	E074	25406
chr1	47069136	47070318	E081	-39010
chr1	47081782	47083126	E081	-26202
chr1	47133179	47134552	E081	23851
chr1	47134569	47134666	E081	25241
chr1	47069136	47070318	E082	-39010
chr1	47081782	47083126	E082	-26202
chr1	47133179	47134552	E082	23851
chr1	47134569	47134666	E082	25241