rs2842576

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

NRDC : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0066 (1976/29892,GnomAD)
C==0083 (2429/29118,TOPMED)
C==0062 (310/5008,1000G)
C==0071 (274/3854,ALSPAC)
C==0081 (302/3708,TWINSUK)

Position: chr1:51858556 (GRCh38.p7) (1p32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 60 Enhancers around

Promoter: 29 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.51858556C>T
GRCh37.p13 chr 1	NC_000001.10:g.52324228C>T
NRDC RefSeqGene	NG_029171.1:g.25382G>A

Gene: NRDC, nardilysin convertase(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NRDC transcript variant 2	NM_001101662.1:c.	N/A	Intron Variant
NRDC transcript variant 3	NM_001242361.1:c.	N/A	Intron Variant
NRDC transcript variant 1	NM_002525.2:c.	N/A	Intron Variant
NRDC transcript variant X1	XM_011541522.1:c.	N/A	Intron Variant
NRDC transcript variant X3	XM_011541523.1:c.	N/A	Intron Variant
NRDC transcript variant X6	XM_011541525.2:c.	N/A	Intron Variant
NRDC transcript variant X4	XM_017001375.1:c.	N/A	Intron Variant
NRDC transcript variant X4	XM_005270903.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.090	T=0.910
1000Genomes	American	Sub	694	C=0.080	T=0.920
1000Genomes	East Asian	Sub	1008	C=0.000	T=1.000
1000Genomes	Europe	Sub	1006	C=0.086	T=0.914
1000Genomes	Global	Study-wide	5008	C=0.062	T=0.938
1000Genomes	South Asian	Sub	978	C=0.050	T=0.950
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.071	T=0.929
The Genome Aggregation Database	African	Sub	8704	C=0.089	T=0.911
The Genome Aggregation Database	American	Sub	836	C=0.070	T=0.930
The Genome Aggregation Database	East Asian	Sub	1620	C=0.000	T=1.000
The Genome Aggregation Database	Europe	Sub	18430	C=0.060	T=0.939
The Genome Aggregation Database	Global	Study-wide	29892	C=0.066	T=0.933
The Genome Aggregation Database	Other	Sub	302	C=0.110	T=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.083	T=0.916
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.081	T=0.919

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res
20202923	A genome-wide association study of alcohol dependence.	Bierut LJ	Proc Natl Acad Sci U S A
21956439	Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.	Zuo L	Neuropsychopharmacology

P-Value

SNP ID	p-value	Traits	Study
rs2842576	0.00000607	alcohol dependence	20202923
rs2842576	0.0000079	alcohol dependence	21703634
rs2842576	0.00025	alcohol dependence	21956439

eQTL of rs2842576 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 rs2842576 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	52316300	52316761	E067	-7467
chr1	52316975	52317070	E067	-7158
chr1	52338905	52338971	E067	14677
chr1	52340942	52341075	E067	16714
chr1	52372063	52372291	E067	47835
chr1	52372622	52372672	E067	48394
chr1	52372693	52372807	E067	48465
chr1	52372854	52373035	E067	48626
chr1	52316300	52316761	E068	-7467
chr1	52325067	52325127	E068	839
chr1	52340429	52340523	E068	16201
chr1	52340942	52341075	E068	16714
chr1	52342170	52342210	E068	17942
chr1	52345606	52345673	E068	21378
chr1	52371811	52371947	E068	47583
chr1	52372063	52372291	E068	47835
chr1	52372622	52372672	E068	48394
chr1	52372693	52372807	E068	48465
chr1	52372854	52373035	E068	48626
chr1	52316300	52316761	E069	-7467
chr1	52316975	52317070	E069	-7158
chr1	52340942	52341075	E069	16714
chr1	52371811	52371947	E069	47583
chr1	52372063	52372291	E069	47835
chr1	52342170	52342210	E070	17942
chr1	52371811	52371947	E070	47583
chr1	52372063	52372291	E070	47835
chr1	52310838	52311008	E071	-13220
chr1	52316300	52316761	E071	-7467
chr1	52316975	52317070	E071	-7158
chr1	52342170	52342210	E071	17942
chr1	52372063	52372291	E071	47835
chr1	52372622	52372672	E071	48394
chr1	52372693	52372807	E071	48465
chr1	52372854	52373035	E071	48626
chr1	52316300	52316761	E072	-7467
chr1	52316975	52317070	E072	-7158
chr1	52325067	52325127	E072	839
chr1	52340429	52340523	E072	16201
chr1	52340942	52341075	E072	16714
chr1	52371811	52371947	E072	47583
chr1	52372063	52372291	E072	47835
chr1	52372622	52372672	E072	48394
chr1	52372693	52372807	E072	48465
chr1	52316300	52316761	E073	-7467
chr1	52284328	52284416	E074	-39812
chr1	52316300	52316761	E074	-7467
chr1	52316975	52317070	E074	-7158
chr1	52325067	52325127	E074	839
chr1	52342170	52342210	E074	17942
chr1	52371811	52371947	E074	47583
chr1	52372063	52372291	E074	47835
chr1	52372622	52372672	E074	48394
chr1	52372693	52372807	E074	48465
chr1	52372854	52373035	E074	48626
chr1	52373095	52373213	E074	48867
chr1	52342170	52342210	E081	17942
chr1	52345606	52345673	E081	21378
chr1	52340429	52340523	E082	16201
chr1	52340942	52341075	E082	16714

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	52343114	52343225	E067	18886
chr1	52343244	52343329	E067	19016
chr1	52343370	52345442	E067	19142
chr1	52343114	52343225	E068	18886
chr1	52343244	52343329	E068	19016
chr1	52343370	52345442	E068	19142
chr1	52343114	52343225	E069	18886
chr1	52343244	52343329	E069	19016
chr1	52343370	52345442	E069	19142
chr1	52343114	52343225	E070	18886
chr1	52343244	52343329	E070	19016
chr1	52343370	52345442	E070	19142
chr1	52343114	52343225	E071	18886
chr1	52343244	52343329	E071	19016
chr1	52343370	52345442	E071	19142
chr1	52343114	52343225	E072	18886
chr1	52343244	52343329	E072	19016
chr1	52343370	52345442	E072	19142
chr1	52343114	52343225	E073	18886
chr1	52343244	52343329	E073	19016
chr1	52343370	52345442	E073	19142
chr1	52343114	52343225	E074	18886
chr1	52343244	52343329	E074	19016
chr1	52343370	52345442	E074	19142
chr1	52343114	52343225	E081	18886
chr1	52343244	52343329	E081	19016
chr1	52343114	52343225	E082	18886
chr1	52343244	52343329	E082	19016
chr1	52343370	52345442	E082	19142