rs2594978

Homo sapiens
C>A
ATG7 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0128 (3847/29916,GnomAD)
C==0130 (3810/29118,TOPMED)
C==0083 (415/5008,1000G)
C==0171 (658/3854,ALSPAC)
C==0185 (686/3708,TWINSUK)
chr3:11341873 (GRCh38.p7) (3p25.3)
ND
GWASdb2
1   publication(s)
See rs on genome
127 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.11341873C>A
GRCh37.p13 chr 3NC_000003.11:g.11383347C>A

Gene: ATG7, autophagy related 7(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ATG7 transcript variant 2NM_001136031.2:c.N/AIntron Variant
ATG7 transcript variant 3NM_001144912.1:c.N/AIntron Variant
ATG7 transcript variant 1NM_006395.2:c.N/AIntron Variant
ATG7 transcript variant X2XM_006712931.3:c.N/AIntron Variant
ATG7 transcript variant X3XM_006712932.3:c.N/AIntron Variant
ATG7 transcript variant X6XM_006712933.3:c.N/AIntron Variant
ATG7 transcript variant X1XM_011533277.2:c.N/AIntron Variant
ATG7 transcript variant X5XM_011533278.2:c.N/AIntron Variant
ATG7 transcript variant X7XM_011533279.2:c.N/AIntron Variant
ATG7 transcript variant X9XM_011533280.2:c.N/AIntron Variant
ATG7 transcript variant X11XM_011533281.2:c.N/AIntron Variant
ATG7 transcript variant X11XM_011533282.2:c.N/AIntron Variant
ATG7 transcript variant X13XM_011533283.2:c.N/AIntron Variant
ATG7 transcript variant X17XM_011533284.2:c.N/AIntron Variant
ATG7 transcript variant X21XM_011533285.2:c.N/AIntron Variant
ATG7 transcript variant X21XM_011533286.2:c.N/AIntron Variant
ATG7 transcript variant X4XM_017005542.1:c.N/AIntron Variant
ATG7 transcript variant X10XM_017005543.1:c.N/AIntron Variant
ATG7 transcript variant X12XM_017005544.1:c.N/AIntron Variant
ATG7 transcript variant X13XM_017005545.1:c.N/AIntron Variant
ATG7 transcript variant X14XM_017005546.1:c.N/AIntron Variant
ATG7 transcript variant X15XM_017005547.1:c.N/AIntron Variant
ATG7 transcript variant X14XM_017005548.1:c.N/AIntron Variant
ATG7 transcript variant X22XM_017005549.1:c.N/AIntron Variant
ATG7 transcript variant X20XM_017005550.1:c.N/AIntron Variant
ATG7 transcript variant X22XM_017005551.1:c.N/AIntron Variant
ATG7 transcript variant X26XM_017005552.1:c.N/AIntron Variant
ATG7 transcript variant X27XM_017005553.1:c.N/AIntron Variant
ATG7 transcript variant X28XM_017005554.1:c.N/AIntron Variant
ATG7 transcript variant X19XR_001739980.1:n.N/AIntron Variant
ATG7 transcript variant X15XR_940363.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.049A=0.951
1000GenomesAmericanSub694C=0.120A=0.880
1000GenomesEast AsianSub1008C=0.000A=1.000
1000GenomesEuropeSub1006C=0.202A=0.798
1000GenomesGlobalStudy-wide5008C=0.083A=0.917
1000GenomesSouth AsianSub978C=0.070A=0.930
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.171A=0.829
The Genome Aggregation DatabaseAfricanSub8718C=0.072A=0.928
The Genome Aggregation DatabaseAmericanSub838C=0.110A=0.890
The Genome Aggregation DatabaseEast AsianSub1618C=0.001A=0.999
The Genome Aggregation DatabaseEuropeSub18440C=0.165A=0.834
The Genome Aggregation DatabaseGlobalStudy-wide29916C=0.128A=0.871
The Genome Aggregation DatabaseOtherSub302C=0.280A=0.720
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.130A=0.869
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.185A=0.815
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs25949780.000413nicotine dependence17158188

eQTL of rs2594978 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 rs2594978 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 )
chr31134833511348622E067-34725
chr31134870111348785E067-34562
chr31134881811349081E067-34266
chr31136446411364650E067-18697
chr31136521511365292E067-18055
chr31136536311365559E067-17788
chr31140780611408096E06724459
chr31141247011412688E06729123
chr31141274111412799E06729394
chr31142079911422278E06737452
chr31142692511427188E06743578
chr31142730211427366E06743955
chr31133338211333677E068-49670
chr31133375111333871E068-49476
chr31134708111347244E068-36103
chr31134736411347424E068-35923
chr31134758111347679E068-35668
chr31134780711347993E068-35354
chr31134833511348622E068-34725
chr31134870111348785E068-34562
chr31136446411364650E068-18697
chr31136521511365292E068-18055
chr31140530011405551E06821953
chr31140575911405960E06822412
chr31140780611408096E06824459
chr31140810711409164E06824760
chr31140937711409441E06826030
chr31141247011412688E06829123
chr31141274111412799E06829394
chr31142079911422278E06837452
chr31142692511427188E06843578
chr31142730211427366E06843955
chr31142747611427617E06844129
chr31143229211432619E06848945
chr31134708111347244E069-36103
chr31134736411347424E069-35923
chr31134758111347679E069-35668
chr31134780711347993E069-35354
chr31134833511348622E069-34725
chr31134870111348785E069-34562
chr31140780611408096E06924459
chr31140810711409164E06924760
chr31140937711409441E06926030
chr31140977311409940E06926426
chr31141123811411282E06927891
chr31141144011411510E06928093
chr31141165611412198E06928309
chr31141231811412368E06928971
chr31142692511427188E06943578
chr31142730211427366E06943955
chr31143229211432619E06948945
chr31135372711353899E070-29448
chr31135392311354006E070-29341
chr31136446411364650E070-18697
chr31136521511365292E070-18055
chr31136536311365559E070-17788
chr31142079911422278E07037452
chr31134708111347244E071-36103
chr31134736411347424E071-35923
chr31134758111347679E071-35668
chr31134780711347993E071-35354
chr31134833511348622E071-34725
chr31134870111348785E071-34562
chr31134881811349081E071-34266
chr31134923711349390E071-33957
chr31136521511365292E071-18055
chr31136536311365559E071-17788
chr31140780611408096E07124459
chr31140810711409164E07124760
chr31142058611420670E07137239
chr31142079911422278E07137452
chr31142692511427188E07143578
chr31142730211427366E07143955
chr31142747611427617E07144129
chr31143229211432619E07148945
chr31134708111347244E072-36103
chr31134736411347424E072-35923
chr31134758111347679E072-35668
chr31134780711347993E072-35354
chr31134833511348622E072-34725
chr31134870111348785E072-34562
chr31134881811349081E072-34266
chr31137643411376784E072-6563
chr31142692511427188E07243578
chr31142730211427366E07243955
chr31143229211432619E07248945
chr31133338211333677E073-49670
chr31134833511348622E073-34725
chr31134870111348785E073-34562
chr31134881811349081E073-34266
chr31134923711349390E073-33957
chr31136521511365292E073-18055
chr31136536311365559E073-17788
chr31140810711409164E07324760
chr31140937711409441E07326030
chr31141290011413046E07329553
chr31141310611413570E07329759
chr31142079911422278E07337452
chr31143229211432619E07348945
chr31134708111347244E074-36103
chr31134736411347424E074-35923
chr31134833511348622E074-34725
chr31134870111348785E074-34562
chr31134881811349081E074-34266
chr31136446411364650E074-18697
chr31136521511365292E074-18055
chr31136536311365559E074-17788
chr31140937711409441E07426030
chr31140977311409940E07426426
chr31141090511410959E07427558
chr31141123811411282E07427891
chr31141247011412688E07429123
chr31141274111412799E07429394
chr31142079911422278E07437452
chr31143206211432207E07448715
chr31143229211432619E07448945
chr31140810711409164E08124760
chr31143091211431458E08147565
chr31143175911431943E08148412
chr31143206211432207E08148715
chr31143229211432619E08148945
chr31135372711353899E082-29448
chr31135392311354006E082-29341
chr31142262711422754E08239280
chr31142278711422913E08239440
chr31143206211432207E08248715
chr31143229211432619E08248945