rs2594995

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ATG7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0128 (3851/29978,GnomAD)
G==0130 (3795/29118,TOPMED)
G==0081 (408/5008,1000G)
G==0171 (658/3854,ALSPAC)
G==0185 (685/3708,TWINSUK)

Position: chr3:11327643 (GRCh38.p7) (3p25.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 153 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.11327643G>A
GRCh37.p13 chr 3	NC_000003.11:g.11369117G>A

Gene: ATG7, autophagy related 7(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATG7 transcript variant 2	NM_001136031.2:c.	N/A	Intron Variant
ATG7 transcript variant 3	NM_001144912.1:c.	N/A	Intron Variant
ATG7 transcript variant 1	NM_006395.2:c.	N/A	Intron Variant
ATG7 transcript variant X2	XM_006712931.3:c.	N/A	Intron Variant
ATG7 transcript variant X3	XM_006712932.3:c.	N/A	Intron Variant
ATG7 transcript variant X6	XM_006712933.3:c.	N/A	Intron Variant
ATG7 transcript variant X1	XM_011533277.2:c.	N/A	Intron Variant
ATG7 transcript variant X5	XM_011533278.2:c.	N/A	Intron Variant
ATG7 transcript variant X7	XM_011533279.2:c.	N/A	Intron Variant
ATG7 transcript variant X9	XM_011533280.2:c.	N/A	Intron Variant
ATG7 transcript variant X11	XM_011533281.2:c.	N/A	Intron Variant
ATG7 transcript variant X11	XM_011533282.2:c.	N/A	Intron Variant
ATG7 transcript variant X13	XM_011533283.2:c.	N/A	Intron Variant
ATG7 transcript variant X17	XM_011533284.2:c.	N/A	Intron Variant
ATG7 transcript variant X21	XM_011533285.2:c.	N/A	Intron Variant
ATG7 transcript variant X21	XM_011533286.2:c.	N/A	Intron Variant
ATG7 transcript variant X4	XM_017005542.1:c.	N/A	Intron Variant
ATG7 transcript variant X10	XM_017005543.1:c.	N/A	Intron Variant
ATG7 transcript variant X12	XM_017005544.1:c.	N/A	Intron Variant
ATG7 transcript variant X13	XM_017005545.1:c.	N/A	Intron Variant
ATG7 transcript variant X14	XM_017005546.1:c.	N/A	Intron Variant
ATG7 transcript variant X15	XM_017005547.1:c.	N/A	Intron Variant
ATG7 transcript variant X14	XM_017005548.1:c.	N/A	Intron Variant
ATG7 transcript variant X22	XM_017005549.1:c.	N/A	Intron Variant
ATG7 transcript variant X20	XM_017005550.1:c.	N/A	Intron Variant
ATG7 transcript variant X22	XM_017005551.1:c.	N/A	Intron Variant
ATG7 transcript variant X26	XM_017005552.1:c.	N/A	Intron Variant
ATG7 transcript variant X27	XM_017005553.1:c.	N/A	Intron Variant
ATG7 transcript variant X28	XM_017005554.1:c.	N/A	Intron Variant
ATG7 transcript variant X19	XR_001739980.1:n.	N/A	Intron Variant
ATG7 transcript variant X15	XR_940363.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.049	A=0.951
1000Genomes	American	Sub	694	G=0.110	A=0.890
1000Genomes	East Asian	Sub	1008	G=0.000	A=1.000
1000Genomes	Europe	Sub	1006	G=0.199	A=0.801
1000Genomes	Global	Study-wide	5008	G=0.081	A=0.919
1000Genomes	South Asian	Sub	978	G=0.070	A=0.930
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.171	A=0.829
The Genome Aggregation Database	African	Sub	8726	G=0.072	A=0.928
The Genome Aggregation Database	American	Sub	836	G=0.110	A=0.890
The Genome Aggregation Database	East Asian	Sub	1616	G=0.001	A=0.999
The Genome Aggregation Database	Europe	Sub	18498	G=0.165	A=0.835
The Genome Aggregation Database	Global	Study-wide	29978	G=0.128	A=0.871
The Genome Aggregation Database	Other	Sub	302	G=0.280	A=0.720
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.130	A=0.869
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.185	A=0.815

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
rs2594995	0.000406	nicotine dependence	17158188

eQTL of rs2594995 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 rs2594995 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 )
chr3	11320494	11320960	E067	-48157
chr3	11320973	11321033	E067	-48084
chr3	11324153	11324287	E067	-44830
chr3	11324294	11324417	E067	-44700
chr3	11324456	11325046	E067	-44071
chr3	11325048	11325259	E067	-43858
chr3	11329677	11331398	E067	-37719
chr3	11348335	11348622	E067	-20495
chr3	11348701	11348785	E067	-20332
chr3	11348818	11349081	E067	-20036
chr3	11364464	11364650	E067	-4467
chr3	11365215	11365292	E067	-3825
chr3	11365363	11365559	E067	-3558
chr3	11407806	11408096	E067	38689
chr3	11412470	11412688	E067	43353
chr3	11412741	11412799	E067	43624
chr3	11320494	11320960	E068	-48157
chr3	11320973	11321033	E068	-48084
chr3	11323534	11323708	E068	-45409
chr3	11324153	11324287	E068	-44830
chr3	11325048	11325259	E068	-43858
chr3	11327821	11327871	E068	-41246
chr3	11329185	11329323	E068	-39794
chr3	11329677	11331398	E068	-37719
chr3	11332884	11333329	E068	-35788
chr3	11333382	11333677	E068	-35440
chr3	11333751	11333871	E068	-35246
chr3	11347081	11347244	E068	-21873
chr3	11347364	11347424	E068	-21693
chr3	11347581	11347679	E068	-21438
chr3	11347807	11347993	E068	-21124
chr3	11348335	11348622	E068	-20495
chr3	11348701	11348785	E068	-20332
chr3	11364464	11364650	E068	-4467
chr3	11365215	11365292	E068	-3825
chr3	11405300	11405551	E068	36183
chr3	11405759	11405960	E068	36642
chr3	11407806	11408096	E068	38689
chr3	11408107	11409164	E068	38990
chr3	11409377	11409441	E068	40260
chr3	11412470	11412688	E068	43353
chr3	11412741	11412799	E068	43624
chr3	11320494	11320960	E069	-48157
chr3	11320973	11321033	E069	-48084
chr3	11323534	11323708	E069	-45409
chr3	11325048	11325259	E069	-43858
chr3	11327220	11327316	E069	-41801
chr3	11327821	11327871	E069	-41246
chr3	11329677	11331398	E069	-37719
chr3	11332884	11333329	E069	-35788
chr3	11347081	11347244	E069	-21873
chr3	11347364	11347424	E069	-21693
chr3	11347581	11347679	E069	-21438
chr3	11347807	11347993	E069	-21124
chr3	11348335	11348622	E069	-20495
chr3	11348701	11348785	E069	-20332
chr3	11407806	11408096	E069	38689
chr3	11408107	11409164	E069	38990
chr3	11409377	11409441	E069	40260
chr3	11409773	11409940	E069	40656
chr3	11411238	11411282	E069	42121
chr3	11411440	11411510	E069	42323
chr3	11411656	11412198	E069	42539
chr3	11412318	11412368	E069	43201
chr3	11324153	11324287	E070	-44830
chr3	11324294	11324417	E070	-44700
chr3	11324456	11325046	E070	-44071
chr3	11353727	11353899	E070	-15218
chr3	11353923	11354006	E070	-15111
chr3	11364464	11364650	E070	-4467
chr3	11365215	11365292	E070	-3825
chr3	11365363	11365559	E070	-3558
chr3	11323534	11323708	E071	-45409
chr3	11324153	11324287	E071	-44830
chr3	11324294	11324417	E071	-44700
chr3	11327220	11327316	E071	-41801
chr3	11327821	11327871	E071	-41246
chr3	11329185	11329323	E071	-39794
chr3	11329677	11331398	E071	-37719
chr3	11331587	11331684	E071	-37433
chr3	11331707	11331804	E071	-37313
chr3	11347081	11347244	E071	-21873
chr3	11347364	11347424	E071	-21693
chr3	11347581	11347679	E071	-21438
chr3	11347807	11347993	E071	-21124
chr3	11348335	11348622	E071	-20495
chr3	11348701	11348785	E071	-20332
chr3	11348818	11349081	E071	-20036
chr3	11349237	11349390	E071	-19727
chr3	11365215	11365292	E071	-3825
chr3	11365363	11365559	E071	-3558
chr3	11407806	11408096	E071	38689
chr3	11408107	11409164	E071	38990
chr3	11320494	11320960	E072	-48157
chr3	11323534	11323708	E072	-45409
chr3	11324153	11324287	E072	-44830
chr3	11325048	11325259	E072	-43858
chr3	11327821	11327871	E072	-41246
chr3	11329185	11329323	E072	-39794
chr3	11329677	11331398	E072	-37719
chr3	11347081	11347244	E072	-21873
chr3	11347364	11347424	E072	-21693
chr3	11347581	11347679	E072	-21438
chr3	11347807	11347993	E072	-21124
chr3	11348335	11348622	E072	-20495
chr3	11348701	11348785	E072	-20332
chr3	11348818	11349081	E072	-20036
chr3	11376434	11376784	E072	7317
chr3	11320494	11320960	E073	-48157
chr3	11323534	11323708	E073	-45409
chr3	11324456	11325046	E073	-44071
chr3	11325048	11325259	E073	-43858
chr3	11329185	11329323	E073	-39794
chr3	11329677	11331398	E073	-37719
chr3	11332884	11333329	E073	-35788
chr3	11333382	11333677	E073	-35440
chr3	11348335	11348622	E073	-20495
chr3	11348701	11348785	E073	-20332
chr3	11348818	11349081	E073	-20036
chr3	11349237	11349390	E073	-19727
chr3	11365215	11365292	E073	-3825
chr3	11365363	11365559	E073	-3558
chr3	11408107	11409164	E073	38990
chr3	11409377	11409441	E073	40260
chr3	11412900	11413046	E073	43783
chr3	11413106	11413570	E073	43989
chr3	11320494	11320960	E074	-48157
chr3	11325048	11325259	E074	-43858
chr3	11327220	11327316	E074	-41801
chr3	11327821	11327871	E074	-41246
chr3	11329185	11329323	E074	-39794
chr3	11331707	11331804	E074	-37313
chr3	11347081	11347244	E074	-21873
chr3	11347364	11347424	E074	-21693
chr3	11348335	11348622	E074	-20495
chr3	11348701	11348785	E074	-20332
chr3	11348818	11349081	E074	-20036
chr3	11364464	11364650	E074	-4467
chr3	11365215	11365292	E074	-3825
chr3	11365363	11365559	E074	-3558
chr3	11409377	11409441	E074	40260
chr3	11409773	11409940	E074	40656
chr3	11410905	11410959	E074	41788
chr3	11411238	11411282	E074	42121
chr3	11412470	11412688	E074	43353
chr3	11412741	11412799	E074	43624
chr3	11324456	11325046	E081	-44071
chr3	11325048	11325259	E081	-43858
chr3	11408107	11409164	E081	38990
chr3	11324294	11324417	E082	-44700
chr3	11324456	11325046	E082	-44071
chr3	11353727	11353899	E082	-15218
chr3	11353923	11354006	E082	-15111