rs28460675

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0147 (4417/29920,GnomAD)
T=0169 (4922/29114,TOPMED)
T=0170 (850/5008,1000G)
T=0122 (470/3854,ALSPAC)
T=0120 (444/3708,TWINSUK)

Position: chr22:49938357 (GRCh38.p7) (22q13.33)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 80 Enhancers around

Promoter: 18 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 22	NC_000022.11:g.49938357G>T
GRCh37.p13 chr 22	NC_000022.10:g.50332005G>T

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.744	T=0.256
1000Genomes	American	Sub	694	G=0.920	T=0.080
1000Genomes	East Asian	Sub	1008	G=0.948	T=0.052
1000Genomes	Europe	Sub	1006	G=0.892	T=0.108
1000Genomes	Global	Study-wide	5008	G=0.830	T=0.170
1000Genomes	South Asian	Sub	978	G=0.700	T=0.300
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.878	T=0.122
The Genome Aggregation Database	African	Sub	8704	G=0.760	T=0.240
The Genome Aggregation Database	American	Sub	838	G=0.920	T=0.080
The Genome Aggregation Database	East Asian	Sub	1620	G=0.949	T=0.051
The Genome Aggregation Database	Europe	Sub	18456	G=0.884	T=0.115
The Genome Aggregation Database	Global	Study-wide	29920	G=0.852	T=0.147
The Genome Aggregation Database	Other	Sub	302	G=0.850	T=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29114	G=0.830	T=0.169
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.880	T=0.120

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

SNP ID	p-value	Traits	Study
rs28460675	9.97E-05	nicotine dependence (smoking)	22377092

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

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 )
chr22	50310498	50310654	E067	-21351
chr22	50310664	50310798	E067	-21207
chr22	50323169	50324139	E067	-7866
chr22	50324156	50325119	E067	-6886
chr22	50332242	50332511	E067	237
chr22	50357710	50364796	E067	25705
chr22	50324156	50325119	E068	-6886
chr22	50326692	50332219	E068	0
chr22	50332242	50332511	E068	237
chr22	50333217	50333380	E068	1212
chr22	50310498	50310654	E069	-21351
chr22	50310664	50310798	E069	-21207
chr22	50323169	50324139	E069	-7866
chr22	50324156	50325119	E069	-6886
chr22	50325150	50325956	E069	-6049
chr22	50326692	50332219	E069	0
chr22	50332242	50332511	E069	237
chr22	50332594	50332720	E069	589
chr22	50332723	50332794	E069	718
chr22	50332852	50332917	E069	847
chr22	50333217	50333380	E069	1212
chr22	50357710	50364796	E069	25705
chr22	50310395	50310445	E070	-21560
chr22	50326692	50332219	E070	0
chr22	50340274	50341177	E070	8269
chr22	50341206	50341515	E070	9201
chr22	50341554	50341703	E070	9549
chr22	50344038	50345628	E070	12033
chr22	50310395	50310445	E071	-21560
chr22	50310498	50310654	E071	-21351
chr22	50310664	50310798	E071	-21207
chr22	50323169	50324139	E071	-7866
chr22	50324156	50325119	E071	-6886
chr22	50325150	50325956	E071	-6049
chr22	50332242	50332511	E071	237
chr22	50332594	50332720	E071	589
chr22	50332723	50332794	E071	718
chr22	50357710	50364796	E071	25705
chr22	50283321	50283381	E072	-48624
chr22	50294906	50295021	E072	-36984
chr22	50295068	50295367	E072	-36638
chr22	50310498	50310654	E072	-21351
chr22	50310664	50310798	E072	-21207
chr22	50323169	50324139	E072	-7866
chr22	50324156	50325119	E072	-6886
chr22	50326692	50332219	E072	0
chr22	50332242	50332511	E072	237
chr22	50332594	50332720	E072	589
chr22	50357710	50364796	E072	25705
chr22	50294906	50295021	E073	-36984
chr22	50295068	50295367	E073	-36638
chr22	50323169	50324139	E073	-7866
chr22	50324156	50325119	E073	-6886
chr22	50326692	50332219	E073	0
chr22	50332242	50332511	E073	237
chr22	50333217	50333380	E073	1212
chr22	50357710	50364796	E073	25705
chr22	50323169	50324139	E074	-7866
chr22	50324156	50325119	E074	-6886
chr22	50325150	50325956	E074	-6049
chr22	50326692	50332219	E074	0
chr22	50332242	50332511	E074	237
chr22	50332594	50332720	E074	589
chr22	50332723	50332794	E074	718
chr22	50357710	50364796	E074	25705
chr22	50285936	50286009	E081	-45996
chr22	50286027	50286178	E081	-45827
chr22	50286270	50286376	E081	-45629
chr22	50286870	50286927	E081	-45078
chr22	50310395	50310445	E081	-21560
chr22	50310498	50310654	E081	-21351
chr22	50310664	50310798	E081	-21207
chr22	50322719	50322794	E081	-9211
chr22	50322806	50323140	E081	-8865
chr22	50323169	50324139	E081	-7866
chr22	50326692	50332219	E081	0
chr22	50310225	50310275	E082	-21730
chr22	50310318	50310385	E082	-21620
chr22	50310395	50310445	E082	-21560
chr22	50333217	50333380	E082	1212

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr22	50311164	50313510	E067	-18495
chr22	50352612	50357694	E067	20607
chr22	50311164	50313510	E068	-18495
chr22	50352612	50357694	E068	20607
chr22	50311164	50313510	E069	-18495
chr22	50352612	50357694	E069	20607
chr22	50311164	50313510	E070	-18495
chr22	50352612	50357694	E070	20607
chr22	50311164	50313510	E071	-18495
chr22	50352612	50357694	E071	20607
chr22	50311164	50313510	E072	-18495
chr22	50352612	50357694	E072	20607
chr22	50311164	50313510	E073	-18495
chr22	50352612	50357694	E073	20607
chr22	50311164	50313510	E074	-18495
chr22	50352612	50357694	E074	20607
chr22	50311164	50313510	E082	-18495
chr22	50352612	50357694	E082	20607

rs28460675

Genomic Coordinates

Population Frequency

P-Value

eQTL of rs28460675 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs28460675 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)