rs1062158

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

NDFIP1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0327 (9777/29856,GnomAD)
C==0308 (8982/29118,TOPMED)
C==0334 (1672/5008,1000G)
C==0387 (1491/3854,ALSPAC)
C==0382 (1416/3708,TWINSUK)

Position: chr5:142143435 (GRCh38.p7) (5q31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 93 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.142143435C>A
GRCh38.p7 chr 5	NC_000005.10:g.142143435C>T
GRCh37.p13 chr 5	NC_000005.9:g.141523000C>A
GRCh37.p13 chr 5	NC_000005.9:g.141523000C>T

Gene: NDFIP1, Nedd4 family interacting protein 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NDFIP1 transcript	NM_030571.3:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.194	T=0.806
1000Genomes	American	Sub	694	C=0.310	T=0.690
1000Genomes	East Asian	Sub	1008	C=0.364	T=0.636
1000Genomes	Europe	Sub	1006	C=0.380	T=0.620
1000Genomes	Global	Study-wide	5008	C=0.334	T=0.666
1000Genomes	South Asian	Sub	978	C=0.460	T=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.387	T=0.613
The Genome Aggregation Database	African	Sub	8692	C=0.229	A=0.000
The Genome Aggregation Database	American	Sub	838	C=0.310	A=0.00,
The Genome Aggregation Database	East Asian	Sub	1616	C=0.349	A=0.000
The Genome Aggregation Database	Europe	Sub	18408	C=0.373	A=0.000
The Genome Aggregation Database	Global	Study-wide	29856	C=0.327	A=0.000
The Genome Aggregation Database	Other	Sub	302	C=0.280	A=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.308	T=0.691
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.382	T=0.618

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
23094030	Protein-protein interaction analysis highlights additional loci of interest for multiple sclerosis.	Ragnedda G	PLoS One
25308886	Functional relevance for multiple sclerosis-associated genetic variants.	Lin X	Immunogenetics

SNP ID	p-value	Traits	Study
rs1062158	0.000537	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
cg07392085	chr5:141489673	NDFIP1	-0.0332937721107096	1.1316e-10

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 )
chr5	141487642	141487707	E067	-27857
chr5	141500239	141500327	E067	-15237
chr5	141500451	141500501	E067	-15063
chr5	141507676	141507760	E067	-7804
chr5	141508433	141508671	E067	-6893
chr5	141524844	141525300	E067	9280
chr5	141525374	141525437	E067	9810
chr5	141546384	141546452	E067	30820
chr5	141494472	141494553	E068	-21011
chr5	141495582	141495765	E068	-19799
chr5	141495983	141496059	E068	-19505
chr5	141508433	141508671	E068	-6893
chr5	141508902	141508952	E068	-6612
chr5	141524844	141525300	E068	9280
chr5	141525374	141525437	E068	9810
chr5	141487642	141487707	E069	-27857
chr5	141492438	141492491	E069	-23073
chr5	141492653	141492760	E069	-22804
chr5	141494472	141494553	E069	-21011
chr5	141497314	141497741	E069	-17823
chr5	141499989	141500071	E069	-15493
chr5	141500239	141500327	E069	-15237
chr5	141500451	141500501	E069	-15063
chr5	141501853	141501920	E069	-13644
chr5	141507676	141507760	E069	-7804
chr5	141508902	141508952	E069	-6612
chr5	141524844	141525300	E069	9280
chr5	141536434	141536602	E069	20870
chr5	141536645	141536984	E069	21081
chr5	141546384	141546452	E069	30820
chr5	141500451	141500501	E070	-15063
chr5	141487642	141487707	E071	-27857
chr5	141495582	141495765	E071	-19799
chr5	141497314	141497741	E071	-17823
chr5	141497905	141497989	E071	-17575
chr5	141498114	141498323	E071	-17241
chr5	141500239	141500327	E071	-15237
chr5	141500451	141500501	E071	-15063
chr5	141501853	141501920	E071	-13644
chr5	141506900	141507129	E071	-8435
chr5	141507676	141507760	E071	-7804
chr5	141508433	141508671	E071	-6893
chr5	141536434	141536602	E071	20870
chr5	141536645	141536984	E071	21081
chr5	141546384	141546452	E071	30820
chr5	141487642	141487707	E072	-27857
chr5	141495582	141495765	E072	-19799
chr5	141497905	141497989	E072	-17575
chr5	141498114	141498323	E072	-17241
chr5	141498690	141498908	E072	-16656
chr5	141506900	141507129	E072	-8435
chr5	141507676	141507760	E072	-7804
chr5	141508902	141508952	E072	-6612
chr5	141536434	141536602	E072	20870
chr5	141536645	141536984	E072	21081
chr5	141546384	141546452	E072	30820
chr5	141494472	141494553	E073	-21011
chr5	141495582	141495765	E073	-19799
chr5	141495983	141496059	E073	-19505
chr5	141498114	141498323	E073	-17241
chr5	141498690	141498908	E073	-16656
chr5	141500239	141500327	E073	-15237
chr5	141500451	141500501	E073	-15063
chr5	141506900	141507129	E073	-8435
chr5	141507676	141507760	E073	-7804
chr5	141508902	141508952	E073	-6612
chr5	141487642	141487707	E074	-27857
chr5	141494472	141494553	E074	-21011
chr5	141497314	141497741	E074	-17823
chr5	141497905	141497989	E074	-17575
chr5	141498114	141498323	E074	-17241
chr5	141498690	141498908	E074	-16656
chr5	141506900	141507129	E074	-8435
chr5	141507676	141507760	E074	-7804
chr5	141508433	141508671	E074	-6893
chr5	141508902	141508952	E074	-6612
chr5	141525374	141525437	E074	9810
chr5	141525797	141525946	E074	10233
chr5	141546384	141546452	E074	30820
chr5	141486750	141486865	E081	-28699
chr5	141487055	141487620	E081	-27944
chr5	141487642	141487707	E081	-27857
chr5	141532042	141532287	E081	16478
chr5	141535529	141535624	E081	19965
chr5	141536434	141536602	E081	20870
chr5	141536645	141536984	E081	21081
chr5	141548955	141549526	E081	33391
chr5	141487055	141487620	E082	-27944
chr5	141507676	141507760	E082	-7804
chr5	141536434	141536602	E082	20870
chr5	141536645	141536984	E082	21081
chr5	141540701	141540800	E082	25137
chr5	141540875	141541088	E082	25311

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	141487834	141490107	E067	-25457
chr5	141487834	141490107	E068	-25457
chr5	141487834	141490107	E069	-25457
chr5	141487834	141490107	E070	-25457
chr5	141487834	141490107	E071	-25457
chr5	141487834	141490107	E072	-25457
chr5	141487834	141490107	E073	-25457
chr5	141487834	141490107	E074	-25457
chr5	141487834	141490107	E081	-25457
chr5	141487834	141490107	E082	-25457

rs1062158

Genomic Coordinates

Gene: NDFIP1, Nedd4 family interacting protein 1(plus strand)

Population Frequency

P-Value

eQTL of rs1062158 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs1062158 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)