rs41453452

Organism: Homo sapiens

Alleles: G>C

Gene : Feature

LOC105378901 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0016 (494/29974,GnomAD)
C=0021 (614/29118,TOPMED)
C=0048 (242/5008,1000G)
C=0014 (54/3854,ALSPAC)
C=0010 (38/3708,TWINSUK)

Position: chr1:110752428 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 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.110752428G>C
GRCh37.p13 chr 1	NC_000001.10:g.111295050G>C

Gene: LOC105378901, uncharacterized LOC105378901(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378901 transcript	XR_001737801.1:n....XR_001737801.1:n.542C>G	C>G	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.992	C=0.008
1000Genomes	American	Sub	694	G=0.990	C=0.010
1000Genomes	East Asian	Sub	1008	G=0.867	C=0.133
1000Genomes	Europe	Sub	1006	G=0.987	C=0.013
1000Genomes	Global	Study-wide	5008	G=0.952	C=0.048
1000Genomes	South Asian	Sub	978	G=0.920	C=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.986	C=0.014
The Genome Aggregation Database	African	Sub	8722	G=0.989	C=0.011
The Genome Aggregation Database	American	Sub	836	G=0.980	C=0.020
The Genome Aggregation Database	East Asian	Sub	1620	G=0.883	C=0.117
The Genome Aggregation Database	Europe	Sub	18494	G=0.990	C=0.009
The Genome Aggregation Database	Global	Study-wide	29974	G=0.983	C=0.016
The Genome Aggregation Database	Other	Sub	302	G=0.970	C=0.030
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.978	C=0.021
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.990	C=0.010

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
rs41453452	0.000309	alcohol dependence	21314694

eQTL of rs41453452 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 rs41453452 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	4100
chr1	111255744	111255892	E068	-39158
chr1	111269454	111269647	E068	-25403
chr1	111269905	111270318	E068	-24732
chr1	111276874	111277170	E068	-17880
chr1	111299150	111299424	E068	4100
chr1	111308623	111308744	E068	13573
chr1	111308755	111308976	E068	13705
chr1	111308977	111309095	E068	13927
chr1	111255744	111255892	E069	-39158
chr1	111257457	111257559	E069	-37491
chr1	111293087	111293549	E069	-1501
chr1	111299150	111299424	E069	4100
chr1	111259934	111260024	E070	-35026
chr1	111261245	111261316	E070	-33734
chr1	111269454	111269647	E070	-25403
chr1	111269905	111270318	E070	-24732
chr1	111276874	111277170	E070	-17880
chr1	111279623	111279678	E070	-15372
chr1	111279761	111279821	E070	-15229
chr1	111279824	111279911	E070	-15139
chr1	111279950	111280197	E070	-14853
chr1	111287286	111287326	E070	-7724
chr1	111292626	111292771	E070	-2279
chr1	111293087	111293549	E070	-1501
chr1	111294256	111294313	E070	-737
chr1	111303016	111303320	E070	7966
chr1	111308336	111308544	E070	13286
chr1	111308623	111308744	E070	13573
chr1	111308755	111308976	E070	13705
chr1	111319055	111319095	E070	24005
chr1	111319348	111319502	E070	24298
chr1	111319934	111320047	E070	24884
chr1	111323277	111323912	E070	28227
chr1	111249155	111249676	E071	-45374
chr1	111257457	111257559	E071	-37491
chr1	111269454	111269647	E071	-25403
chr1	111255744	111255892	E072	-39158
chr1	111257457	111257559	E072	-37491
chr1	111292626	111292771	E072	-2279
chr1	111257457	111257559	E073	-37491
chr1	111255744	111255892	E074	-39158
chr1	111269905	111270318	E074	-24732
chr1	111299150	111299424	E074	4100
chr1	111257457	111257559	E081	-37491
chr1	111261245	111261316	E081	-33734
chr1	111269454	111269647	E081	-25403
chr1	111269905	111270318	E081	-24732
chr1	111276874	111277170	E081	-17880
chr1	111292626	111292771	E081	-2279
chr1	111293087	111293549	E081	-1501
chr1	111294256	111294313	E081	-737
chr1	111308623	111308744	E081	13573
chr1	111319055	111319095	E081	24005
chr1	111323277	111323912	E081	28227
chr1	111269905	111270318	E082	-24732
chr1	111276874	111277170	E082	-17880
chr1	111292626	111292771	E082	-2279
chr1	111293087	111293549	E082	-1501
chr1	111294256	111294313	E082	-737