rs4416887

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

PCSK5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0271 (8118/29938,GnomAD)
A==0308 (8967/29118,TOPMED)
A==0300 (1501/5008,1000G)
A==0251 (967/3854,ALSPAC)
A==0255 (945/3708,TWINSUK)

Position: chr9:75982309 (GRCh38.p7) (9q21.13)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 70 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.75982309A>G
GRCh38.p7 chr 9	NC_000009.12:g.75982309A>T
GRCh37.p13 chr 9	NC_000009.11:g.78597225A>G
GRCh37.p13 chr 9	NC_000009.11:g.78597225A>T
PCSK5 RefSeqGene	NG_029445.1:g.96666A>G
PCSK5 RefSeqGene	NG_029445.1:g.96666A>T

Gene: PCSK5, proprotein convertase subtilisin/kexin type 5(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PCSK5 transcript variant 1	NM_001190482.1:c.	N/A	Intron Variant
PCSK5 transcript variant 2	NM_006200.5:c.	N/A	Intron Variant
PCSK5 transcript variant 3	NR_120409.1:n.	N/A	Intron Variant
PCSK5 transcript variant X1	XM_005252039.3:c.	N/A	Intron Variant
PCSK5 transcript variant X2	XM_011518769.2:c.	N/A	Intron Variant
PCSK5 transcript variant X3	XM_011518770.2:c.	N/A	Genic Upstream Transcript Variant
PCSK5 transcript variant X4	XM_017014800.1:c.	N/A	Genic Upstream Transcript Variant
PCSK5 transcript variant X5	XR_929806.1:n.	N/A	Intron Variant
PCSK5 transcript variant X6	XR_929807.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.412	G=0.588
1000Genomes	American	Sub	694	A=0.240	G=0.760
1000Genomes	East Asian	Sub	1008	A=0.166	G=0.834
1000Genomes	Europe	Sub	1006	A=0.282	G=0.718
1000Genomes	Global	Study-wide	5008	A=0.300	G=0.700
1000Genomes	South Asian	Sub	978	A=0.350	G=0.650
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.251	G=0.749
The Genome Aggregation Database	African	Sub	8706	A=0.375	G=0.625
The Genome Aggregation Database	American	Sub	834	A=0.220	G=0.780
The Genome Aggregation Database	East Asian	Sub	1616	A=0.154	G=0.846
The Genome Aggregation Database	Europe	Sub	18480	A=0.234	G=0.766
The Genome Aggregation Database	Global	Study-wide	29938	A=0.271	G=0.728
The Genome Aggregation Database	Other	Sub	302	A=0.320	G=0.680
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.308	G=0.692
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.255	G=0.745

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs4416887	3.96E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs4416887 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 rs4416887 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 )
chr9	117109900	117110012	E067	38687
chr9	117110206	117110302	E067	38993
chr9	117110406	117110476	E067	39193
chr9	117110564	117110659	E067	39351
chr9	117110684	117110847	E067	39471
chr9	117109900	117110012	E068	38687
chr9	117110206	117110302	E068	38993
chr9	117110406	117110476	E068	39193
chr9	117110564	117110659	E068	39351
chr9	117110684	117110847	E068	39471
chr9	117110872	117111957	E068	39659
chr9	117111982	117112464	E068	40769
chr9	117052878	117053714	E069	-17499
chr9	117053718	117053814	E069	-17399
chr9	117067775	117068416	E069	-2797
chr9	117109900	117110012	E069	38687
chr9	117110206	117110302	E069	38993
chr9	117110406	117110476	E069	39193
chr9	117110564	117110659	E069	39351
chr9	117110684	117110847	E069	39471
chr9	117110872	117111957	E069	39659
chr9	117021878	117022722	E070	-48491
chr9	117022743	117022793	E070	-48420
chr9	117022799	117022849	E070	-48364
chr9	117067615	117067676	E070	-3537
chr9	117067775	117068416	E070	-2797
chr9	117081552	117081651	E070	10339
chr9	117081822	117081882	E070	10609
chr9	117033955	117034130	E071	-37083
chr9	117034138	117034380	E071	-36833
chr9	117067775	117068416	E071	-2797
chr9	117068419	117068586	E071	-2627
chr9	117109900	117110012	E071	38687
chr9	117110206	117110302	E071	38993
chr9	117110406	117110476	E071	39193
chr9	117110564	117110659	E071	39351
chr9	117110684	117110847	E071	39471
chr9	117110872	117111957	E071	39659
chr9	117052878	117053714	E072	-17499
chr9	117053718	117053814	E072	-17399
chr9	117067615	117067676	E072	-3537
chr9	117109900	117110012	E072	38687
chr9	117110206	117110302	E072	38993
chr9	117110406	117110476	E072	39193
chr9	117110564	117110659	E072	39351
chr9	117110684	117110847	E072	39471
chr9	117110872	117111957	E072	39659
chr9	117067775	117068416	E073	-2797
chr9	117110872	117111957	E073	39659
chr9	117067775	117068416	E074	-2797
chr9	117109900	117110012	E074	38687
chr9	117110206	117110302	E074	38993
chr9	117110406	117110476	E074	39193
chr9	117110564	117110659	E074	39351
chr9	117110684	117110847	E074	39471
chr9	117110872	117111957	E074	39659
chr9	117021506	117021700	E081	-49513
chr9	117021760	117021810	E081	-49403
chr9	117021878	117022722	E081	-48491
chr9	117022743	117022793	E081	-48420
chr9	117022799	117022849	E081	-48364
chr9	117052878	117053714	E081	-17499
chr9	117067775	117068416	E081	-2797
chr9	117068419	117068586	E081	-2627
chr9	117021506	117021700	E082	-49513
chr9	117021760	117021810	E082	-49403
chr9	117049720	117049779	E082	-21434
chr9	117049839	117049985	E082	-21228
chr9	117052755	117052848	E082	-18365
chr9	117052878	117053714	E082	-17499