rs7046144

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PRUNE2 : Intron Variant
LOC105376095 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0050 (1510/29988,GnomAD)
C==0050 (1460/29118,TOPMED)
C==0085 (426/5008,1000G)
C==0052 (202/3854,ALSPAC)
C==0047 (174/3708,TWINSUK)

Position: chr9:76616633 (GRCh38.p7) (9q21.2)

Phenotype: ND

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 9	NC_000009.12:g.76616633C>T
GRCh37.p13 chr 9	NC_000009.11:g.79231549C>T

Gene: PRUNE2, prune homolog 2 (Drosophila)(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PRUNE2 transcript variant 2	NM_001308047.1:c.	N/A	Intron Variant
PRUNE2 transcript variant 3	NM_001308048.1:c.	N/A	Intron Variant
PRUNE2 transcript variant 4	NM_001308049.1:c.	N/A	Intron Variant
PRUNE2 transcript variant 5	NM_001308050.1:c.	N/A	Intron Variant
PRUNE2 transcript variant 6	NM_001308051.1:c.	N/A	Intron Variant
PRUNE2 transcript variant 1	NM_015225.2:c.	N/A	Intron Variant
PRUNE2 transcript variant 7	NR_131751.1:n.	N/A	Intron Variant
PRUNE2 transcript variant X7	XM_005251745.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X8	XM_005251746.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X10	XM_005251748.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X13	XM_005251750.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X20	XM_005251751.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X28	XM_005251754.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X1	XM_006716982.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X2	XM_006716983.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X4	XM_006716984.2:c.	N/A	Intron Variant
PRUNE2 transcript variant X5	XM_006716985.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X6	XM_006716986.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X11	XM_011518323.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X16	XM_011518326.2:c.	N/A	Intron Variant
PRUNE2 transcript variant X17	XM_011518327.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X24	XM_011518328.2:c.	N/A	Intron Variant
PRUNE2 transcript variant X9	XM_017014345.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X14	XM_017014346.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X18	XM_017014347.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X19	XM_017014348.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X21	XM_017014349.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X22	XM_017014350.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X25	XM_017014351.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X26	XM_017014352.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X29	XM_017014354.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X30	XM_017014355.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X31	XM_017014356.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X32	XM_017014357.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X33	XM_017014358.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X34	XM_017014359.1:c.	N/A	Intron Variant
PRUNE2 transcript variant X27	XM_017014353.1:c.	N/A	Genic Downstream Transcript Variant
PRUNE2 transcript variant X12	XR_001746209.1:n.	N/A	Intron Variant
PRUNE2 transcript variant X15	XR_001746210.1:n.	N/A	Intron Variant
PRUNE2 transcript variant X23	XR_001746211.1:n.	N/A	Intron Variant
PRUNE2 transcript variant X35	XR_001746212.1:n.	N/A	Intron Variant
PRUNE2 transcript variant X3	XR_428517.2:n.	N/A	Intron Variant

Gene: LOC105376095, uncharacterized LOC105376095(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105376095 transcript variant X1	XR_001746738.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X2	XR_001746739.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X3	XR_001746740.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X4	XR_001746741.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X5	XR_001746742.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X6	XR_001746743.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X7	XR_001746744.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X8	XR_001746745.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X9	XR_001746746.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X10	XR_001746747.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X11	XR_001746748.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X12	XR_001746749.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X13	XR_001746750.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X14	XR_001746751.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X7	XR_001746752.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X12	XR_001746753.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X13	XR_001746754.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X18	XR_001746755.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X19	XR_001746756.1:n.	N/A	Intron Variant
LOC105376095 transcript variant X21	XR_001746757.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.049	T=0.951
1000Genomes	American	Sub	694	C=0.040	T=0.960
1000Genomes	East Asian	Sub	1008	C=0.093	T=0.907
1000Genomes	Europe	Sub	1006	C=0.048	T=0.952
1000Genomes	Global	Study-wide	5008	C=0.085	T=0.915
1000Genomes	South Asian	Sub	978	C=0.200	T=0.800
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.052	T=0.948
The Genome Aggregation Database	African	Sub	8728	C=0.047	T=0.953
The Genome Aggregation Database	American	Sub	838	C=0.040	T=0.960
The Genome Aggregation Database	East Asian	Sub	1616	C=0.072	T=0.928
The Genome Aggregation Database	Europe	Sub	18504	C=0.049	T=0.950
The Genome Aggregation Database	Global	Study-wide	29988	C=0.050	T=0.949
The Genome Aggregation Database	Other	Sub	302	C=0.120	T=0.880
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.050	T=0.949
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.047	T=0.953

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

P-Value

SNP ID	p-value	Traits	Study
rs7046144	0.000465	nicotine dependence	17158188

eQTL of rs7046144 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 rs7046144 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	79261133	79261536	E067	29584
chr9	79269501	79269907	E067	37952
chr9	79269956	79270580	E067	38407
chr9	79223557	79225373	E068	-6176
chr9	79253009	79253308	E068	21460
chr9	79257518	79257780	E068	25969
chr9	79257796	79257847	E068	26247
chr9	79257857	79258024	E068	26308
chr9	79258038	79258166	E068	26489
chr9	79258346	79258954	E068	26797
chr9	79258968	79259094	E068	27419
chr9	79265600	79266749	E068	34051
chr9	79239025	79239173	E069	7476
chr9	79269956	79270580	E069	38407
chr9	79206807	79206988	E070	-24561
chr9	79207012	79208261	E070	-23288
chr9	79215047	79215126	E070	-16423
chr9	79217887	79217937	E070	-13612
chr9	79218344	79218818	E070	-12731
chr9	79218863	79219159	E070	-12390
chr9	79223557	79225373	E071	-6176
chr9	79253009	79253308	E071	21460
chr9	79261133	79261536	E071	29584
chr9	79269956	79270580	E071	38407
chr9	79274091	79274141	E071	42542
chr9	79253009	79253308	E072	21460
chr9	79261133	79261536	E072	29584
chr9	79269046	79269206	E072	37497
chr9	79261133	79261536	E073	29584
chr9	79223557	79225373	E074	-6176
chr9	79253009	79253308	E074	21460
chr9	79257857	79258024	E074	26308
chr9	79258038	79258166	E074	26489
chr9	79269215	79269479	E074	37666
chr9	79269501	79269907	E074	37952
chr9	79200531	79202194	E081	-29355
chr9	79202399	79202449	E081	-29100
chr9	79202732	79202786	E081	-28763
chr9	79211188	79211303	E081	-20246
chr9	79211317	79211673	E081	-19876
chr9	79217221	79217425	E081	-14124
chr9	79217887	79217937	E081	-13612
chr9	79218344	79218818	E081	-12731
chr9	79218863	79219159	E081	-12390
chr9	79235440	79235563	E081	3891
chr9	79235579	79235849	E081	4030
chr9	79235922	79236207	E081	4373
chr9	79236294	79236344	E081	4745
chr9	79238491	79238677	E081	6942
chr9	79238678	79238901	E081	7129
chr9	79239025	79239173	E081	7476
chr9	79239275	79239979	E081	7726
chr9	79218863	79219159	E082	-12390
chr9	79235440	79235563	E082	3891
chr9	79235579	79235849	E082	4030
chr9	79235922	79236207	E082	4373
chr9	79236294	79236344	E082	4745
chr9	79238678	79238901	E082	7129
chr9	79239025	79239173	E082	7476
chr9	79239275	79239979	E082	7726