rs2606742

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ATG7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0194 (5840/29964,GnomAD)
G==0233 (6794/29118,TOPMED)
G==0160 (803/5008,1000G)
G==0171 (658/3854,ALSPAC)
G==0187 (693/3708,TWINSUK)

Position: chr3:11350243 (GRCh38.p7) (3p25.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 137 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.11350243G>A
GRCh37.p13 chr 3	NC_000003.11:g.11391717G>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=0.334	A=0.666
1000Genomes	American	Sub	694	G=0.140	A=0.860
1000Genomes	East Asian	Sub	1008	G=0.000	A=1.000
1000Genomes	Europe	Sub	1006	G=0.200	A=0.800
1000Genomes	Global	Study-wide	5008	G=0.160	A=0.840
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	8716	G=0.298	A=0.702
The Genome Aggregation Database	American	Sub	838	G=0.130	A=0.870
The Genome Aggregation Database	East Asian	Sub	1622	G=0.001	A=0.999
The Genome Aggregation Database	Europe	Sub	18486	G=0.164	A=0.835
The Genome Aggregation Database	Global	Study-wide	29964	G=0.194	A=0.805
The Genome Aggregation Database	Other	Sub	302	G=0.280	A=0.720
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.233	A=0.766
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.187	A=0.813

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
rs2606742	0.00058	nicotine dependence	17158188

eQTL of rs2606742 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 rs2606742 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	11348335	11348622	E067	-43095
chr3	11348701	11348785	E067	-42932
chr3	11348818	11349081	E067	-42636
chr3	11364464	11364650	E067	-27067
chr3	11365215	11365292	E067	-26425
chr3	11365363	11365559	E067	-26158
chr3	11407806	11408096	E067	16089
chr3	11412470	11412688	E067	20753
chr3	11412741	11412799	E067	21024
chr3	11420799	11422278	E067	29082
chr3	11426925	11427188	E067	35208
chr3	11427302	11427366	E067	35585
chr3	11347081	11347244	E068	-44473
chr3	11347364	11347424	E068	-44293
chr3	11347581	11347679	E068	-44038
chr3	11347807	11347993	E068	-43724
chr3	11348335	11348622	E068	-43095
chr3	11348701	11348785	E068	-42932
chr3	11364464	11364650	E068	-27067
chr3	11365215	11365292	E068	-26425
chr3	11405300	11405551	E068	13583
chr3	11405759	11405960	E068	14042
chr3	11407806	11408096	E068	16089
chr3	11408107	11409164	E068	16390
chr3	11409377	11409441	E068	17660
chr3	11412470	11412688	E068	20753
chr3	11412741	11412799	E068	21024
chr3	11420799	11422278	E068	29082
chr3	11426925	11427188	E068	35208
chr3	11427302	11427366	E068	35585
chr3	11427476	11427617	E068	35759
chr3	11432292	11432619	E068	40575
chr3	11432746	11433370	E068	41029
chr3	11347081	11347244	E069	-44473
chr3	11347364	11347424	E069	-44293
chr3	11347581	11347679	E069	-44038
chr3	11347807	11347993	E069	-43724
chr3	11348335	11348622	E069	-43095
chr3	11348701	11348785	E069	-42932
chr3	11407806	11408096	E069	16089
chr3	11408107	11409164	E069	16390
chr3	11409377	11409441	E069	17660
chr3	11409773	11409940	E069	18056
chr3	11411238	11411282	E069	19521
chr3	11411440	11411510	E069	19723
chr3	11411656	11412198	E069	19939
chr3	11412318	11412368	E069	20601
chr3	11426925	11427188	E069	35208
chr3	11427302	11427366	E069	35585
chr3	11432292	11432619	E069	40575
chr3	11432746	11433370	E069	41029
chr3	11433444	11434560	E069	41727
chr3	11353727	11353899	E070	-37818
chr3	11353923	11354006	E070	-37711
chr3	11364464	11364650	E070	-27067
chr3	11365215	11365292	E070	-26425
chr3	11365363	11365559	E070	-26158
chr3	11420799	11422278	E070	29082
chr3	11432746	11433370	E070	41029
chr3	11347081	11347244	E071	-44473
chr3	11347364	11347424	E071	-44293
chr3	11347581	11347679	E071	-44038
chr3	11347807	11347993	E071	-43724
chr3	11348335	11348622	E071	-43095
chr3	11348701	11348785	E071	-42932
chr3	11348818	11349081	E071	-42636
chr3	11349237	11349390	E071	-42327
chr3	11365215	11365292	E071	-26425
chr3	11365363	11365559	E071	-26158
chr3	11407806	11408096	E071	16089
chr3	11408107	11409164	E071	16390
chr3	11420586	11420670	E071	28869
chr3	11420799	11422278	E071	29082
chr3	11426925	11427188	E071	35208
chr3	11427302	11427366	E071	35585
chr3	11427476	11427617	E071	35759
chr3	11432292	11432619	E071	40575
chr3	11432746	11433370	E071	41029
chr3	11433444	11434560	E071	41727
chr3	11347081	11347244	E072	-44473
chr3	11347364	11347424	E072	-44293
chr3	11347581	11347679	E072	-44038
chr3	11347807	11347993	E072	-43724
chr3	11348335	11348622	E072	-43095
chr3	11348701	11348785	E072	-42932
chr3	11348818	11349081	E072	-42636
chr3	11376434	11376784	E072	-14933
chr3	11426925	11427188	E072	35208
chr3	11427302	11427366	E072	35585
chr3	11432292	11432619	E072	40575
chr3	11432746	11433370	E072	41029
chr3	11348335	11348622	E073	-43095
chr3	11348701	11348785	E073	-42932
chr3	11348818	11349081	E073	-42636
chr3	11349237	11349390	E073	-42327
chr3	11365215	11365292	E073	-26425
chr3	11365363	11365559	E073	-26158
chr3	11408107	11409164	E073	16390
chr3	11409377	11409441	E073	17660
chr3	11412900	11413046	E073	21183
chr3	11413106	11413570	E073	21389
chr3	11420799	11422278	E073	29082
chr3	11432292	11432619	E073	40575
chr3	11432746	11433370	E073	41029
chr3	11433444	11434560	E073	41727
chr3	11347081	11347244	E074	-44473
chr3	11347364	11347424	E074	-44293
chr3	11348335	11348622	E074	-43095
chr3	11348701	11348785	E074	-42932
chr3	11348818	11349081	E074	-42636
chr3	11364464	11364650	E074	-27067
chr3	11365215	11365292	E074	-26425
chr3	11365363	11365559	E074	-26158
chr3	11409377	11409441	E074	17660
chr3	11409773	11409940	E074	18056
chr3	11410905	11410959	E074	19188
chr3	11411238	11411282	E074	19521
chr3	11412470	11412688	E074	20753
chr3	11412741	11412799	E074	21024
chr3	11420799	11422278	E074	29082
chr3	11432062	11432207	E074	40345
chr3	11432292	11432619	E074	40575
chr3	11432746	11433370	E074	41029
chr3	11408107	11409164	E081	16390
chr3	11430912	11431458	E081	39195
chr3	11431759	11431943	E081	40042
chr3	11432062	11432207	E081	40345
chr3	11432292	11432619	E081	40575
chr3	11432746	11433370	E081	41029
chr3	11433444	11434560	E081	41727
chr3	11353727	11353899	E082	-37818
chr3	11353923	11354006	E082	-37711
chr3	11422627	11422754	E082	30910
chr3	11422787	11422913	E082	31070
chr3	11432062	11432207	E082	40345
chr3	11432292	11432619	E082	40575
chr3	11432746	11433370	E082	41029