rs6563354

Homo sapiens
C>T
DCLK1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0307 (9185/29922,GnomAD)
T=0323 (9424/29116,TOPMED)
T=0358 (1794/5008,1000G)
T=0236 (908/3854,ALSPAC)
T=0231 (855/3708,TWINSUK)
chr13:36122357 (GRCh38.p7) (13q13.3)
AD
GWASdb2
1   publication(s)
See rs on genome
98 Enhancers around
46 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.36122357C>T
GRCh37.p13 chr 13NC_000013.10:g.36696494C>T

Gene: DCLK1, doublecortin like kinase 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
DCLK1 transcript variant 1NM_004734.4:c.N/AIntron Variant
DCLK1 transcript variant 2NM_001195415.1:c.N/AGenic Upstream Transcript Variant
DCLK1 transcript variant 3NM_001195416.1:c.N/AGenic Upstream Transcript Variant
DCLK1 transcript variant 4NM_001195430.1:c.N/AGenic Upstream Transcript Variant
DCLK1 transcript variant X1XM_005266592.2:c.N/AIntron Variant
DCLK1 transcript variant X2XM_006719893.2:c.N/AIntron Variant
DCLK1 transcript variant X1XM_017020847.1:c.N/AIntron Variant
DCLK1 transcript variant X2XM_017020848.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.564T=0.436
1000GenomesAmericanSub694C=0.700T=0.300
1000GenomesEast AsianSub1008C=0.647T=0.353
1000GenomesEuropeSub1006C=0.759T=0.241
1000GenomesGlobalStudy-wide5008C=0.642T=0.358
1000GenomesSouth AsianSub978C=0.580T=0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.764T=0.236
The Genome Aggregation DatabaseAfricanSub8690C=0.576T=0.424
The Genome Aggregation DatabaseAmericanSub838C=0.680T=0.320
The Genome Aggregation DatabaseEast AsianSub1618C=0.678T=0.322
The Genome Aggregation DatabaseEuropeSub18474C=0.750T=0.249
The Genome Aggregation DatabaseGlobalStudy-wide29922C=0.693T=0.307
The Genome Aggregation DatabaseOtherSub302C=0.670T=0.330
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.676T=0.323
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.769T=0.231
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
rs65633540.000392alcohol dependence20201924

eQTL of rs6563354 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 rs6563354 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 )
chr133669826436698866E0671770
chr133670106936701379E0674575
chr133666337536663667E068-32827
chr133666371336663930E068-32564
chr133669821836698262E0681724
chr133669826436698866E0681770
chr133669821836698262E0691724
chr133670079636700886E0694302
chr133670106936701379E0694575
chr133665059536650648E070-45846
chr133665091236650962E070-45532
chr133667025236670460E070-26034
chr133667046536670627E070-25867
chr133667065036671186E070-25308
chr133667119936671300E070-25194
chr133667142236671472E070-25022
chr133667454836674601E070-21893
chr133667527836675810E070-20684
chr133667799036678105E070-18389
chr133667836736678537E070-17957
chr133669584536695885E070-609
chr133669613036696180E070-314
chr133669936536699438E0702871
chr133669988636699960E0703392
chr133670079636700886E0704302
chr133670106936701379E0704575
chr133670155836701651E0705064
chr133670773936707894E07011245
chr133670809036708140E07011596
chr133670820236708372E07011708
chr133670850736708619E07012013
chr133670891136709020E07012417
chr133673151036732291E07035016
chr133673697636737080E07040482
chr133673721536737291E07040721
chr133673887936738969E07042385
chr133673907036739172E07042576
chr133667799036678105E071-18389
chr133666259436662644E072-33850
chr133666289536663058E072-33436
chr133666337536663667E072-32827
chr133666371336663930E072-32564
chr133666394336664134E072-32360
chr133666424036664290E072-32204
chr133666430336664551E072-31943
chr133667799036678105E072-18389
chr133667836736678537E072-17957
chr133667836736678537E073-17957
chr133669060236690652E073-5842
chr133669821836698262E0731724
chr133669826436698866E0731770
chr133669886936698938E0732375
chr133670079636700886E0734302
chr133670106936701379E0734575
chr133667836736678537E074-17957
chr133664822236648319E081-48175
chr133664976536649815E081-46679
chr133665006936650138E081-46356
chr133665059536650648E081-45846
chr133666902136669145E081-27349
chr133667025236670460E081-26034
chr133667046536670627E081-25867
chr133667065036671186E081-25308
chr133667119936671300E081-25194
chr133667799036678105E081-18389
chr133667836736678537E081-17957
chr133668182836683474E081-13020
chr133668804236688120E081-8374
chr133669584536695885E081-609
chr133669826436698866E0811770
chr133669886936698938E0812375
chr133669936536699438E0812871
chr133669988636699960E0813392
chr133670079636700886E0814302
chr133670106936701379E0814575
chr133670155836701651E0815064
chr133673743936738671E08140945
chr133664976536649815E082-46679
chr133666860336668725E082-27769
chr133666878136668976E082-27518
chr133666902136669145E082-27349
chr133667025236670460E082-26034
chr133667046536670627E082-25867
chr133667065036671186E082-25308
chr133667119936671300E082-25194
chr133667231636672517E082-23977
chr133667527836675810E082-20684
chr133667891436678999E082-17495
chr133669584536695885E082-609
chr133669613036696180E082-314
chr133669936536699438E0822871
chr133669988636699960E0823392
chr133670079636700886E0824302
chr133670106936701379E0824575
chr133670155836701651E0825064
chr133670809036708140E08211596
chr133673721536737291E08240721
chr133673743936738671E08240945










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr133670381236703913E0677318
chr133670398836704261E0677494
chr133670437336705894E0677879
chr133672869836729614E06732204
chr133670381236703913E0687318
chr133670398836704261E0687494
chr133670437336705894E0687879
chr133672869836729614E06832204
chr133670381236703913E0697318
chr133670398836704261E0697494
chr133670437336705894E0697879
chr133672869836729614E06932204
chr133670329636703407E0706802
chr133670353736703592E0707043
chr133670381236703913E0707318
chr133670398836704261E0707494
chr133670437336705894E0707879
chr133672869836729614E07032204
chr133670381236703913E0717318
chr133670398836704261E0717494
chr133670437336705894E0717879
chr133672869836729614E07132204
chr133670329636703407E0726802
chr133670353736703592E0727043
chr133670381236703913E0727318
chr133670398836704261E0727494
chr133670437336705894E0727879
chr133672869836729614E07232204
chr133670329636703407E0736802
chr133670353736703592E0737043
chr133670381236703913E0737318
chr133670398836704261E0737494
chr133670437336705894E0737879
chr133672869836729614E07332204
chr133670398836704261E0747494
chr133670437336705894E0747879
chr133670353736703592E0817043
chr133670381236703913E0817318
chr133670398836704261E0817494
chr133670437336705894E0817879
chr133670329636703407E0826802
chr133670353736703592E0827043
chr133670381236703913E0827318
chr133670398836704261E0827494
chr133670437336705894E0827879
chr133672869836729614E08232204