rs420033

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105378901 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0188 (5633/29958,GnomAD)
A=0180 (5266/29118,TOPMED)
A=0165 (827/5008,1000G)
A=0263 (1015/3854,ALSPAC)
A=0275 (1019/3708,TWINSUK)

Position: chr1:110753052 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 60 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.110753052G>A
GRCh37.p13 chr 1	NC_000001.10:g.111295674G>A

Gene: LOC105378901, uncharacterized LOC105378901(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378901 transcript	XR_001737801.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.973	A=0.027
1000Genomes	American	Sub	694	G=0.750	A=0.250
1000Genomes	East Asian	Sub	1008	G=0.867	A=0.133
1000Genomes	Europe	Sub	1006	G=0.722	A=0.278
1000Genomes	Global	Study-wide	5008	G=0.835	A=0.165
1000Genomes	South Asian	Sub	978	G=0.790	A=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.737	A=0.263
The Genome Aggregation Database	African	Sub	8716	G=0.936	A=0.064
The Genome Aggregation Database	American	Sub	838	G=0.790	A=0.210
The Genome Aggregation Database	East Asian	Sub	1616	G=0.863	A=0.137
The Genome Aggregation Database	Europe	Sub	18486	G=0.753	A=0.246
The Genome Aggregation Database	Global	Study-wide	29958	G=0.812	A=0.188
The Genome Aggregation Database	Other	Sub	302	G=0.610	A=0.390
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.819	A=0.180
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.725	A=0.275

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs420033	6.17E-05	alcohol dependence	19581569

eQTL of rs420033 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 rs420033 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	111299150	111299424	E067	3476
chr1	111255744	111255892	E068	-39782
chr1	111269454	111269647	E068	-26027
chr1	111269905	111270318	E068	-25356
chr1	111276874	111277170	E068	-18504
chr1	111299150	111299424	E068	3476
chr1	111308623	111308744	E068	12949
chr1	111308755	111308976	E068	13081
chr1	111308977	111309095	E068	13303
chr1	111255744	111255892	E069	-39782
chr1	111257457	111257559	E069	-38115
chr1	111293087	111293549	E069	-2125
chr1	111299150	111299424	E069	3476
chr1	111259934	111260024	E070	-35650
chr1	111261245	111261316	E070	-34358
chr1	111269454	111269647	E070	-26027
chr1	111269905	111270318	E070	-25356
chr1	111276874	111277170	E070	-18504
chr1	111279623	111279678	E070	-15996
chr1	111279761	111279821	E070	-15853
chr1	111279824	111279911	E070	-15763
chr1	111279950	111280197	E070	-15477
chr1	111287286	111287326	E070	-8348
chr1	111292626	111292771	E070	-2903
chr1	111293087	111293549	E070	-2125
chr1	111294256	111294313	E070	-1361
chr1	111303016	111303320	E070	7342
chr1	111308336	111308544	E070	12662
chr1	111308623	111308744	E070	12949
chr1	111308755	111308976	E070	13081
chr1	111319055	111319095	E070	23381
chr1	111319348	111319502	E070	23674
chr1	111319934	111320047	E070	24260
chr1	111323277	111323912	E070	27603
chr1	111249155	111249676	E071	-45998
chr1	111257457	111257559	E071	-38115
chr1	111269454	111269647	E071	-26027
chr1	111255744	111255892	E072	-39782
chr1	111257457	111257559	E072	-38115
chr1	111292626	111292771	E072	-2903
chr1	111257457	111257559	E073	-38115
chr1	111255744	111255892	E074	-39782
chr1	111269905	111270318	E074	-25356
chr1	111299150	111299424	E074	3476
chr1	111257457	111257559	E081	-38115
chr1	111261245	111261316	E081	-34358
chr1	111269454	111269647	E081	-26027
chr1	111269905	111270318	E081	-25356
chr1	111276874	111277170	E081	-18504
chr1	111292626	111292771	E081	-2903
chr1	111293087	111293549	E081	-2125
chr1	111294256	111294313	E081	-1361
chr1	111308623	111308744	E081	12949
chr1	111319055	111319095	E081	23381
chr1	111323277	111323912	E081	27603
chr1	111269905	111270318	E082	-25356
chr1	111276874	111277170	E082	-18504
chr1	111292626	111292771	E082	-2903
chr1	111293087	111293549	E082	-2125
chr1	111294256	111294313	E082	-1361