rs11978979

Homo sapiens
A>T
SDK1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0247 (7403/29916,GnomAD)
T=0227 (6629/29118,TOPMED)
T=0224 (1123/5008,1000G)
T=0274 (1055/3854,ALSPAC)
T=0259 (962/3708,TWINSUK)
chr7:3986377 (GRCh38.p7) (7p22.2)
AD
GWASdb2
1   publication(s)
See rs on genome
103 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.3986377A>T
GRCh37.p13 chr 7NC_000007.13:g.4026009A>T

Gene: SDK1, sidekick cell adhesion molecule 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SDK1 transcript variant 1NM_152744.3:c.N/AIntron Variant
SDK1 transcript variant 2NM_001079653.1:c.N/AGenic Upstream Transcript Variant
SDK1 transcript variant X4XM_011515188.1:c.N/AIntron Variant
SDK1 transcript variant X5XM_011515189.1:c.N/AIntron Variant
SDK1 transcript variant X6XM_011515190.1:c.N/AIntron Variant
SDK1 transcript variant X1XM_017011837.1:c.N/AIntron Variant
SDK1 transcript variant X7XM_017011838.1:c.N/AIntron Variant
SDK1 transcript variant X8XM_017011839.1:c.N/AIntron Variant
SDK1 transcript variant X9XM_017011840.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.818T=0.182
1000GenomesAmericanSub694A=0.730T=0.270
1000GenomesEast AsianSub1008A=0.828T=0.172
1000GenomesEuropeSub1006A=0.780T=0.220
1000GenomesGlobalStudy-wide5008A=0.776T=0.224
1000GenomesSouth AsianSub978A=0.690T=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.726T=0.274
The Genome Aggregation DatabaseAfricanSub8700A=0.799T=0.201
The Genome Aggregation DatabaseAmericanSub838A=0.710T=0.290
The Genome Aggregation DatabaseEast AsianSub1622A=0.860T=0.140
The Genome Aggregation DatabaseEuropeSub18454A=0.723T=0.276
The Genome Aggregation DatabaseGlobalStudy-wide29916A=0.752T=0.247
The Genome Aggregation DatabaseOtherSub302A=0.690T=0.310
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.772T=0.227
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.741T=0.259
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs119789790.000122alcohol dependence21314694

eQTL of rs11978979 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 rs11978979 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 )
chr740646384064802E06738629
chr740648834064933E06738874
chr740649584065108E06738949
chr740651294066014E06739120
chr740312404032037E0685231
chr739994943999567E069-26442
chr740463764046655E06920367
chr740467554047029E06920746
chr740643594064409E06938350
chr740646384064802E06938629
chr740648834064933E06938874
chr740649584065108E06938949
chr740651294066014E06939120
chr739948523995033E070-30976
chr739951913995252E070-30757
chr740312404032037E0705231
chr740463764046655E07020367
chr740467554047029E07020746
chr740470514047145E07021042
chr740488294049651E07022820
chr740496864050488E07023677
chr740506004050681E07024591
chr740508304050893E07024821
chr740508954051318E07024886
chr740513684051476E07025359
chr740515934051696E07025584
chr740528514052901E07026842
chr740530544053168E07027045
chr740533504053682E07027341
chr740536934053857E07027684
chr740538994054010E07027890
chr740541354054240E07028126
chr739981693998280E071-27729
chr739986093998711E071-27298
chr739987863998836E071-27173
chr739994943999567E071-26442
chr740486384048748E07122629
chr740639414064051E07137932
chr740641574064207E07138148
chr740642254064335E07138216
chr740643594064409E07138350
chr740646384064802E07138629
chr740648834064933E07138874
chr740649584065108E07138949
chr740651294066014E07139120
chr740312404032037E0725231
chr740463764046655E07220367
chr740641574064207E07238148
chr740642254064335E07238216
chr740643594064409E07238350
chr740646384064802E07238629
chr740648834064933E07238874
chr740649584065108E07238949
chr740651294066014E07239120
chr739994943999567E074-26442
chr740641574064207E07438148
chr740642254064335E07438216
chr740643594064409E07438350
chr740646384064802E07438629
chr740648834064933E07438874
chr740649584065108E07438949
chr740651294066014E07439120
chr739868253986895E081-39114
chr739882283989468E081-36541
chr739895643989618E081-36391
chr739899113990076E081-35933
chr739998063999916E081-26093
chr739999384000118E081-25891
chr740001234000238E081-25771
chr740003414000480E081-25529
chr740398354040012E08113826
chr740401424040280E08114133
chr740463764046655E08120367
chr740467554047029E08120746
chr740470514047145E08121042
chr740488294049651E08122820
chr740496864050488E08123677
chr740506004050681E08124591
chr740508304050893E08124821
chr740508954051318E08124886
chr740513684051476E08125359
chr740515934051696E08125584
chr740533504053682E08127341
chr740536934053857E08127684
chr740735104073598E08147501
chr740736544073894E08147645
chr740739614074020E08147952
chr740743974074600E08148388
chr740188114018887E082-7122
chr740189624019012E082-6997
chr740463764046655E08220367
chr740467554047029E08220746
chr740470514047145E08221042
chr740484574048511E08222448
chr740486384048748E08222629
chr740488294049651E08222820
chr740496864050488E08223677
chr740506004050681E08224591
chr740508304050893E08224821
chr740508954051318E08224886
chr740513684051476E08225359
chr740515934051696E08225584
chr740619094062378E08235900