rs2290775

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

AKT1S1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0395 (11787/29838,GnomAD)
T=0431 (12577/29118,TOPMED)
T=0388 (1944/5008,1000G)
T=0405 (1559/3854,ALSPAC)
T=0417 (1545/3708,TWINSUK)

Position: chr19:49871985 (GRCh38.p7) (19q13.33)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 96 Enhancers around

Promoter: 36 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.49871985C>T
GRCh37.p13 chr 19	NC_000019.9:g.50375242C>T
PNKP RefSeqGene	NG_027717.1:g.581G>A

Gene: AKT1S1, AKT1 substrate 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AKT1S1 transcript variant 2	NM_001098632.2:c.	N/A	Intron Variant
AKT1S1 transcript variant 3	NM_001098633.3:c.	N/A	Intron Variant
AKT1S1 transcript variant 4	NM_001278159.1:c.	N/A	Intron Variant
AKT1S1 transcript variant 5	NM_001278160.1:c.	N/A	Intron Variant
AKT1S1 transcript variant 1	NM_032375.5:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.561	T=0.439
1000Genomes	American	Sub	694	C=0.720	T=0.280
1000Genomes	East Asian	Sub	1008	C=0.767	T=0.233
1000Genomes	Europe	Sub	1006	C=0.586	T=0.414
1000Genomes	Global	Study-wide	5008	C=0.612	T=0.388
1000Genomes	South Asian	Sub	978	C=0.470	T=0.530
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.595	T=0.405
The Genome Aggregation Database	African	Sub	8662	C=0.555	T=0.445
The Genome Aggregation Database	American	Sub	838	C=0.710	T=0.290
The Genome Aggregation Database	East Asian	Sub	1616	C=0.765	T=0.235
The Genome Aggregation Database	Europe	Sub	18420	C=0.610	T=0.389
The Genome Aggregation Database	Global	Study-wide	29838	C=0.605	T=0.395
The Genome Aggregation Database	Other	Sub	302	C=0.560	T=0.440
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.568	T=0.431
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.583	T=0.417

PMID	Title	Author	Journal
22377092	ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.	Wang KS	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs2290775	5.83E-05	nicotine dependence (smoking)	22377092

eQTL of rs2290775 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:50375242	PNKP	ENSG00000039650.5	C>T	1.1199e-5	4076	Frontal_Cortex_BA9
Chr19:50375242	PNKP	ENSG00000039650.5	C>T	3.0339e-9	4076	Cortex
Chr19:50375242	PNKP	ENSG00000039650.5	C>T	2.4345e-5	4076	Caudate_basal_ganglia
Chr19:50375242	PNKP	ENSG00000039650.5	C>T	4.1939e-5	4076	Anterior_cingulate_cortex
Chr19:50375242	PNKP	ENSG00000039650.5	C>T	3.5947e-3	4076	Nucleus_accumbens_basal_ganglia

meQTL of rs2290775 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg24893721	chr19:50380873	AKT1S1\|TBC1D17	0.0123270535355568	1.8098e-32
cg10751382	chr19:50391554	TBC1D17	0.0433248829367072	2.6435e-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 )
chr19	50357017	50357754	E067	-17488
chr19	50361171	50362583	E067	-12659
chr19	50369162	50369464	E067	-5778
chr19	50371500	50371988	E067	-3254
chr19	50409779	50410106	E067	34537
chr19	50410179	50410232	E067	34937
chr19	50410244	50410387	E067	35002
chr19	50410394	50410444	E067	35152
chr19	50410538	50410638	E067	35296
chr19	50414402	50415056	E067	39160
chr19	50415155	50415311	E067	39913
chr19	50356517	50356633	E068	-18609
chr19	50356767	50356838	E068	-18404
chr19	50357017	50357754	E068	-17488
chr19	50361171	50362583	E068	-12659
chr19	50371500	50371988	E068	-3254
chr19	50407443	50407768	E068	32201
chr19	50409779	50410106	E068	34537
chr19	50410179	50410232	E068	34937
chr19	50410244	50410387	E068	35002
chr19	50410394	50410444	E068	35152
chr19	50410538	50410638	E068	35296
chr19	50414402	50415056	E068	39160
chr19	50356517	50356633	E069	-18609
chr19	50361171	50362583	E069	-12659
chr19	50368248	50368389	E069	-6853
chr19	50368428	50369000	E069	-6242
chr19	50369162	50369464	E069	-5778
chr19	50371500	50371988	E069	-3254
chr19	50377071	50378555	E069	1829
chr19	50409208	50409429	E069	33966
chr19	50409779	50410106	E069	34537
chr19	50410179	50410232	E069	34937
chr19	50410244	50410387	E069	35002
chr19	50410394	50410444	E069	35152
chr19	50410538	50410638	E069	35296
chr19	50410671	50410739	E069	35429
chr19	50357017	50357754	E070	-17488
chr19	50362675	50366772	E070	-8470
chr19	50368428	50369000	E070	-6242
chr19	50369162	50369464	E070	-5778
chr19	50356517	50356633	E071	-18609
chr19	50356767	50356838	E071	-18404
chr19	50356848	50356913	E071	-18329
chr19	50357017	50357754	E071	-17488
chr19	50361171	50362583	E071	-12659
chr19	50368248	50368389	E071	-6853
chr19	50368428	50369000	E071	-6242
chr19	50369162	50369464	E071	-5778
chr19	50371500	50371988	E071	-3254
chr19	50409208	50409429	E071	33966
chr19	50409779	50410106	E071	34537
chr19	50410179	50410232	E071	34937
chr19	50420455	50421000	E071	45213
chr19	50422533	50422618	E071	47291
chr19	50422811	50422917	E071	47569
chr19	50422983	50423027	E071	47741
chr19	50356517	50356633	E072	-18609
chr19	50357017	50357754	E072	-17488
chr19	50361171	50362583	E072	-12659
chr19	50369162	50369464	E072	-5778
chr19	50409208	50409429	E072	33966
chr19	50410244	50410387	E072	35002
chr19	50410394	50410444	E072	35152
chr19	50410538	50410638	E072	35296
chr19	50410671	50410739	E072	35429
chr19	50414305	50414355	E072	39063
chr19	50414402	50415056	E072	39160
chr19	50415155	50415311	E072	39913
chr19	50416178	50416326	E072	40936
chr19	50416383	50416547	E072	41141
chr19	50416576	50416877	E072	41334
chr19	50417029	50417098	E072	41787
chr19	50417151	50417219	E072	41909
chr19	50356517	50356633	E073	-18609
chr19	50356767	50356838	E073	-18404
chr19	50356848	50356913	E073	-18329
chr19	50357017	50357754	E073	-17488
chr19	50360360	50361126	E073	-14116
chr19	50361171	50362583	E073	-12659
chr19	50371500	50371988	E073	-3254
chr19	50361171	50362583	E074	-12659
chr19	50371500	50371988	E074	-3254
chr19	50409208	50409429	E074	33966
chr19	50409779	50410106	E074	34537
chr19	50410179	50410232	E074	34937
chr19	50410244	50410387	E074	35002
chr19	50410394	50410444	E074	35152
chr19	50410538	50410638	E074	35296
chr19	50356517	50356633	E081	-18609
chr19	50356767	50356838	E081	-18404
chr19	50356848	50356913	E081	-18329
chr19	50357017	50357754	E081	-17488
chr19	50368428	50369000	E081	-6242
chr19	50369162	50369464	E081	-5778
chr19	50371500	50371988	E082	-3254

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	50352693	50356342	E067	-18900
chr19	50369566	50371388	E067	-3854
chr19	50372055	50374837	E067	-405
chr19	50378686	50382835	E067	3444
chr19	50352693	50356342	E068	-18900
chr19	50369566	50371388	E068	-3854
chr19	50372055	50374837	E068	-405
chr19	50378686	50382835	E068	3444
chr19	50352693	50356342	E069	-18900
chr19	50369566	50371388	E069	-3854
chr19	50372055	50374837	E069	-405
chr19	50378686	50382835	E069	3444
chr19	50352693	50356342	E070	-18900
chr19	50369566	50371388	E070	-3854
chr19	50372055	50374837	E070	-405
chr19	50378686	50382835	E070	3444
chr19	50352693	50356342	E071	-18900
chr19	50369566	50371388	E071	-3854
chr19	50372055	50374837	E071	-405
chr19	50378686	50382835	E071	3444
chr19	50352693	50356342	E072	-18900
chr19	50369566	50371388	E072	-3854
chr19	50372055	50374837	E072	-405
chr19	50378686	50382835	E072	3444
chr19	50352693	50356342	E073	-18900
chr19	50369566	50371388	E073	-3854
chr19	50372055	50374837	E073	-405
chr19	50378686	50382835	E073	3444
chr19	50352693	50356342	E074	-18900
chr19	50369566	50371388	E074	-3854
chr19	50372055	50374837	E074	-405
chr19	50378686	50382835	E074	3444
chr19	50352693	50356342	E082	-18900
chr19	50369566	50371388	E082	-3854
chr19	50372055	50374837	E082	-405
chr19	50378686	50382835	E082	3444