rs4388209

Homo sapiens
T>C
GRAMD3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0268 (8020/29916,GnomAD)
T==0270 (7861/29118,TOPMED)
T==0338 (1695/5008,1000G)
T==0275 (1060/3854,ALSPAC)
T==0296 (1098/3708,TWINSUK)
chr5:126422681 (GRCh38.p7) (5q23.2)
AD
GWASdb2
1   publication(s)
See rs on genome
240 Enhancers around
37 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.126422681T>C
GRCh37.p13 chr 5NC_000005.9:g.125758373T>C

Gene: GRAMD3, GRAM domain containing 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GRAMD3 transcript variant 1NM_001146319.1:c.N/AIntron Variant
GRAMD3 transcript variant 3NM_001146320.1:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant 4NM_001146321.1:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant 5NM_001146322.1:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant 2NM_023927.2:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant X4XM_005272057.3:c.N/AIntron Variant
GRAMD3 transcript variant X5XM_005272058.3:c.N/AIntron Variant
GRAMD3 transcript variant X11XM_005272062.3:c.N/AIntron Variant
GRAMD2B transcript variant X3XM_011543593.2:c.N/AIntron Variant
GRAMD2B transcript variant X11XM_017009781.1:c.N/AIntron Variant
GRAMD3 transcript variant X6XM_005272059.4:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant X7XM_005272060.3:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant X10XM_005272061.3:c.N/AGenic Upstream Transcript Variant
GRAMD2B transcript variant X8XM_005272063.3:c.N/AGenic Upstream Transcript Variant
GRAMD2B transcript variant X10XM_005272064.3:c.N/AGenic Upstream Transcript Variant
GRAMD2B transcript variant X1XM_011543591.2:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant X2XM_011543592.2:c.N/AGenic Upstream Transcript Variant
GRAMD2B transcript variant X6XM_011543594.2:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant X17XM_011543595.2:c.N/AGenic Upstream Transcript Variant
GRAMD2B transcript variant X12XM_017009782.1:c.N/AGenic Upstream Transcript Variant
GRAMD2B transcript variant X13XM_017009783.1:c.N/AGenic Upstream Transcript Variant
GRAMD2B transcript variant X14XM_017009784.1:c.N/AGenic Upstream Transcript Variant
GRAMD2B transcript variant X15XM_017009785.1:c.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant X8XR_001742219.1:n.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant X9XR_001742220.1:n.N/AGenic Upstream Transcript Variant
GRAMD3 transcript variant X21XR_001742221.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.191C=0.809
1000GenomesAmericanSub694T=0.240C=0.760
1000GenomesEast AsianSub1008T=0.498C=0.502
1000GenomesEuropeSub1006T=0.311C=0.689
1000GenomesGlobalStudy-wide5008T=0.338C=0.662
1000GenomesSouth AsianSub978T=0.470C=0.530
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.275C=0.725
The Genome Aggregation DatabaseAfricanSub8706T=0.234C=0.766
The Genome Aggregation DatabaseAmericanSub838T=0.210C=0.790
The Genome Aggregation DatabaseEast AsianSub1612T=0.476C=0.524
The Genome Aggregation DatabaseEuropeSub18458T=0.267C=0.732
The Genome Aggregation DatabaseGlobalStudy-wide29916T=0.268C=0.731
The Genome Aggregation DatabaseOtherSub302T=0.330C=0.670
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.270C=0.730
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.296C=0.704
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs43882090.00047alcohol dependence20201924

eQTL of rs4388209 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 rs4388209 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 )
chr5125750606125751043E067-7330
chr5125751230125751341E067-7032
chr5125751733125751923E067-6450
chr5125764269125764789E0675896
chr5125768615125768794E06710242
chr5125768911125769015E06710538
chr5125769026125769070E06710653
chr5125770621125770712E06712248
chr5125773508125773752E06715135
chr5125774007125774109E06715634
chr5125774180125774231E06715807
chr5125777079125777252E06718706
chr5125779171125779459E06720798
chr5125782924125782988E06724551
chr5125782995125783045E06724622
chr5125784027125784067E06725654
chr5125784375125784495E06726002
chr5125784558125784684E06726185
chr5125785147125786838E06726774
chr5125789305125789355E06730932
chr5125789861125790021E06731488
chr5125790792125790832E06732419
chr5125791526125791697E06733153
chr5125796766125796976E06738393
chr5125797576125797712E06739203
chr5125797805125797897E06739432
chr5125797968125798209E06739595
chr5125798243125798310E06739870
chr5125805241125805922E06746868
chr5125711826125711946E068-46427
chr5125712256125712412E068-45961
chr5125750223125750280E068-8093
chr5125751230125751341E068-7032
chr5125764269125764789E0685896
chr5125768615125768794E06810242
chr5125768911125769015E06810538
chr5125769026125769070E06810653
chr5125769337125769764E06810964
chr5125770621125770712E06812248
chr5125770837125770887E06812464
chr5125773508125773752E06815135
chr5125776524125776607E06818151
chr5125777079125777252E06818706
chr5125779171125779459E06820798
chr5125779975125780040E06821602
chr5125782924125782988E06824551
chr5125784027125784067E06825654
chr5125784375125784495E06826002
chr5125784558125784684E06826185
chr5125785147125786838E06826774
chr5125786974125787016E06828601
chr5125787033125787110E06828660
chr5125788310125788495E06829937
chr5125789305125789355E06830932
chr5125789861125790021E06831488
chr5125790792125790832E06832419
chr5125791526125791697E06833153
chr5125794403125794455E06836030
chr5125795147125795254E06836774
chr5125796766125796976E06838393
chr5125797576125797712E06839203
chr5125797805125797897E06839432
chr5125797968125798209E06839595
chr5125798243125798310E06839870
chr5125800581125800964E06842208
chr5125807282125807636E06848909
chr5125711826125711946E069-46427
chr5125712256125712412E069-45961
chr5125750606125751043E069-7330
chr5125751230125751341E069-7032
chr5125751733125751923E069-6450
chr5125764269125764789E0695896
chr5125768615125768794E06910242
chr5125768911125769015E06910538
chr5125770621125770712E06912248
chr5125770837125770887E06912464
chr5125773508125773752E06915135
chr5125774007125774109E06915634
chr5125774180125774231E06915807
chr5125777079125777252E06918706
chr5125779171125779459E06920798
chr5125782168125782896E06923795
chr5125782924125782988E06924551
chr5125782995125783045E06924622
chr5125784027125784067E06925654
chr5125784375125784495E06926002
chr5125784558125784684E06926185
chr5125785147125786838E06926774
chr5125786974125787016E06928601
chr5125787033125787110E06928660
chr5125788310125788495E06929937
chr5125789305125789355E06930932
chr5125789861125790021E06931488
chr5125790792125790832E06932419
chr5125791526125791697E06933153
chr5125796766125796976E06938393
chr5125797576125797712E06939203
chr5125797805125797897E06939432
chr5125797968125798209E06939595
chr5125798243125798310E06939870
chr5125799822125800020E06941449
chr5125800581125800964E06942208
chr5125801002125801213E06942629
chr5125807282125807636E06948909
chr5125712256125712412E071-45961
chr5125750223125750280E071-8093
chr5125751230125751341E071-7032
chr5125764269125764789E0715896
chr5125768615125768794E07110242
chr5125768911125769015E07110538
chr5125769026125769070E07110653
chr5125769337125769764E07110964
chr5125770621125770712E07112248
chr5125770837125770887E07112464
chr5125777079125777252E07118706
chr5125779171125779459E07120798
chr5125779975125780040E07121602
chr5125784027125784067E07125654
chr5125784375125784495E07126002
chr5125784558125784684E07126185
chr5125785147125786838E07126774
chr5125786974125787016E07128601
chr5125787033125787110E07128660
chr5125788310125788495E07129937
chr5125789305125789355E07130932
chr5125789861125790021E07131488
chr5125791526125791697E07133153
chr5125792251125792418E07133878
chr5125794403125794455E07136030
chr5125795147125795254E07136774
chr5125796766125796976E07138393
chr5125797805125797897E07139432
chr5125797968125798209E07139595
chr5125798243125798310E07139870
chr5125799822125800020E07141449
chr5125800581125800964E07142208
chr5125801002125801213E07142629
chr5125805241125805922E07146868
chr5125750223125750280E072-8093
chr5125751733125751923E072-6450
chr5125768615125768794E07210242
chr5125768911125769015E07210538
chr5125769026125769070E07210653
chr5125769337125769764E07210964
chr5125770621125770712E07212248
chr5125770837125770887E07212464
chr5125777079125777252E07218706
chr5125784027125784067E07225654
chr5125784375125784495E07226002
chr5125784558125784684E07226185
chr5125785147125786838E07226774
chr5125786974125787016E07228601
chr5125789305125789355E07230932
chr5125789861125790021E07231488
chr5125791526125791697E07233153
chr5125794403125794455E07236030
chr5125796766125796976E07238393
chr5125797576125797712E07239203
chr5125797805125797897E07239432
chr5125797968125798209E07239595
chr5125798243125798310E07239870
chr5125800581125800964E07242208
chr5125801002125801213E07242629
chr5125807282125807636E07248909
chr5125711826125711946E073-46427
chr5125750223125750280E073-8093
chr5125750606125751043E073-7330
chr5125751230125751341E073-7032
chr5125751733125751923E073-6450
chr5125768615125768794E07310242
chr5125768911125769015E07310538
chr5125770621125770712E07312248
chr5125770837125770887E07312464
chr5125774007125774109E07315634
chr5125777079125777252E07318706
chr5125779171125779459E07320798
chr5125784027125784067E07325654
chr5125784375125784495E07326002
chr5125784558125784684E07326185
chr5125785147125786838E07326774
chr5125786974125787016E07328601
chr5125787033125787110E07328660
chr5125788310125788495E07329937
chr5125789305125789355E07330932
chr5125789861125790021E07331488
chr5125790792125790832E07332419
chr5125791526125791697E07333153
chr5125796766125796976E07338393
chr5125797576125797712E07339203
chr5125797805125797897E07339432
chr5125797968125798209E07339595
chr5125798243125798310E07339870
chr5125799822125800020E07341449
chr5125800581125800964E07342208
chr5125807282125807636E07348909
chr5125711826125711946E074-46427
chr5125712256125712412E074-45961
chr5125712455125712505E074-45868
chr5125750223125750280E074-8093
chr5125750606125751043E074-7330
chr5125751230125751341E074-7032
chr5125751733125751923E074-6450
chr5125752781125752841E074-5532
chr5125768615125768794E07410242
chr5125768911125769015E07410538
chr5125769026125769070E07410653
chr5125769337125769764E07410964
chr5125770621125770712E07412248
chr5125770837125770887E07412464
chr5125773508125773752E07415135
chr5125774007125774109E07415634
chr5125774180125774231E07415807
chr5125777079125777252E07418706
chr5125779171125779459E07420798
chr5125779975125780040E07421602
chr5125781820125782076E07423447
chr5125783434125783484E07425061
chr5125784027125784067E07425654
chr5125784375125784495E07426002
chr5125784558125784684E07426185
chr5125785147125786838E07426774
chr5125786974125787016E07428601
chr5125787033125787110E07428660
chr5125788310125788495E07429937
chr5125789305125789355E07430932
chr5125789861125790021E07431488
chr5125790792125790832E07432419
chr5125791526125791697E07433153
chr5125792251125792418E07433878
chr5125792828125792879E07434455
chr5125794403125794455E07436030
chr5125795147125795254E07436774
chr5125796766125796976E07438393
chr5125797576125797712E07439203
chr5125797805125797897E07439432
chr5125797968125798209E07439595
chr5125798243125798310E07439870
chr5125800581125800964E07442208
chr5125801002125801213E07442629
chr5125807282125807636E07448909







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5125758592125759862E067219
chr5125759896125760012E0671523
chr5125760046125760162E0671673
chr5125760290125761186E0671917
chr5125762120125762185E0673747
chr5125758592125759862E068219
chr5125759896125760012E0681523
chr5125760046125760162E0681673
chr5125760290125761186E0681917
chr5125762120125762185E0683747
chr5125758592125759862E069219
chr5125759896125760012E0691523
chr5125760046125760162E0691673
chr5125760290125761186E0691917
chr5125762120125762185E0693747
chr5125758592125759862E070219
chr5125758592125759862E071219
chr5125759896125760012E0711523
chr5125760046125760162E0711673
chr5125760290125761186E0711917
chr5125762120125762185E0713747
chr5125758592125759862E072219
chr5125759896125760012E0721523
chr5125760046125760162E0721673
chr5125760290125761186E0721917
chr5125762120125762185E0723747
chr5125758592125759862E073219
chr5125759896125760012E0731523
chr5125760046125760162E0731673
chr5125760290125761186E0731917
chr5125762120125762185E0733747
chr5125758592125759862E074219
chr5125759896125760012E0741523
chr5125760046125760162E0741673
chr5125760290125761186E0741917
chr5125762120125762185E0743747
chr5125758592125759862E082219