rs4141442

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

NTPCR : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0269 (8080/29950,GnomAD)
C=0287 (8381/29116,TOPMED)
C=0238 (1193/5008,1000G)
C=0261 (1004/3854,ALSPAC)
C=0263 (976/3708,TWINSUK)

Position: chr1:232963129 (GRCh38.p7) (1q42.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 48 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.232963129T>C
GRCh37.p13 chr 1	NC_000001.10:g.233098875T>C

Gene: NTPCR, nucleoside-triphosphatase, cancer-related(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NTPCR transcript	NM_032324.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.670	C=0.330
1000Genomes	American	Sub	694	T=0.830	C=0.170
1000Genomes	East Asian	Sub	1008	T=0.819	C=0.181
1000Genomes	Europe	Sub	1006	T=0.758	C=0.242
1000Genomes	Global	Study-wide	5008	T=0.762	C=0.238
1000Genomes	South Asian	Sub	978	T=0.780	C=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.739	C=0.261
The Genome Aggregation Database	African	Sub	8712	T=0.676	C=0.324
The Genome Aggregation Database	American	Sub	836	T=0.830	C=0.170
The Genome Aggregation Database	East Asian	Sub	1614	T=0.802	C=0.198
The Genome Aggregation Database	Europe	Sub	18486	T=0.745	C=0.254
The Genome Aggregation Database	Global	Study-wide	29950	T=0.730	C=0.269
The Genome Aggregation Database	Other	Sub	302	T=0.690	C=0.310
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.712	C=0.287
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.737	C=0.263

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
rs4141442	0.000755	alcohol dependence	20201924

eQTL of rs4141442 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 rs4141442 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg21690725	chr1:233086060	C1orf57	0.0217295275447843	4.7425e-13

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	233120434	233120637	E067	21559
chr1	233121556	233121682	E067	22681
chr1	233141532	233141765	E067	42657
chr1	233142012	233142102	E067	43137
chr1	233142320	233142701	E067	43445
chr1	233142709	233142882	E067	43834
chr1	233088150	233088200	E068	-10675
chr1	233088595	233088971	E068	-9904
chr1	233120434	233120637	E068	21559
chr1	233142320	233142701	E068	43445
chr1	233142709	233142882	E068	43834
chr1	233088595	233088971	E069	-9904
chr1	233089002	233089262	E069	-9613
chr1	233120434	233120637	E069	21559
chr1	233121556	233121682	E069	22681
chr1	233141532	233141765	E069	42657
chr1	233142012	233142102	E069	43137
chr1	233142320	233142701	E069	43445
chr1	233142709	233142882	E069	43834
chr1	233098598	233099052	E071	0
chr1	233099275	233099409	E071	400
chr1	233104788	233105010	E071	5913
chr1	233120434	233120637	E071	21559
chr1	233141532	233141765	E071	42657
chr1	233142012	233142102	E071	43137
chr1	233142320	233142701	E071	43445
chr1	233142709	233142882	E071	43834
chr1	233088150	233088200	E072	-10675
chr1	233088595	233088971	E072	-9904
chr1	233120434	233120637	E072	21559
chr1	233121556	233121682	E072	22681
chr1	233141532	233141765	E072	42657
chr1	233142012	233142102	E072	43137
chr1	233142320	233142701	E072	43445
chr1	233142709	233142882	E072	43834
chr1	233085356	233085400	E073	-13475
chr1	233120434	233120637	E074	21559
chr1	233121556	233121682	E074	22681
chr1	233142012	233142102	E074	43137
chr1	233142320	233142701	E074	43445
chr1	233142709	233142882	E074	43834
chr1	233102458	233102741	E081	3583
chr1	233103016	233103101	E081	4141
chr1	233116250	233116331	E081	17375
chr1	233116467	233116584	E081	17592
chr1	233116765	233116815	E081	17890
chr1	233102458	233102741	E082	3583
chr1	233116467	233116584	E082	17592

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	233085804	233087353	E067	-11522
chr1	233085804	233087353	E068	-11522
chr1	233085804	233087353	E069	-11522
chr1	233085804	233087353	E070	-11522
chr1	233085804	233087353	E071	-11522
chr1	233085804	233087353	E072	-11522
chr1	233085804	233087353	E073	-11522
chr1	233085804	233087353	E074	-11522
chr1	233085804	233087353	E081	-11522
chr1	233085804	233087353	E082	-11522