rs619672

Homo sapiens
G>A
SDK1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0342 (10240/29932,GnomAD)
A=0408 (11895/29118,TOPMED)
A=0321 (1609/5008,1000G)
A=0230 (887/3854,ALSPAC)
A=0227 (840/3708,TWINSUK)
chr7:4156356 (GRCh38.p7) (7p22.2)
ND
GWASdb2
1   publication(s)
See rs on genome
70 Enhancers around
1 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.4156356G>A
GRCh37.p13 chr 7NC_000007.13:g.4195988G>A

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

Molecule type Change Amino acid[Codon] SO Term
SDK1 transcript variant 2NM_001079653.1:c.N/AIntron Variant
SDK1 transcript variant 1NM_152744.3:c.N/AIntron 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
1000GenomesAfricanSub1322G=0.272A=0.728
1000GenomesAmericanSub694G=0.740A=0.260
1000GenomesEast AsianSub1008G=0.997A=0.003
1000GenomesEuropeSub1006G=0.772A=0.228
1000GenomesGlobalStudy-wide5008G=0.679A=0.321
1000GenomesSouth AsianSub978G=0.760A=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.770A=0.230
The Genome Aggregation DatabaseAfricanSub8708G=0.346A=0.654
The Genome Aggregation DatabaseAmericanSub838G=0.800A=0.200
The Genome Aggregation DatabaseEast AsianSub1620G=0.994A=0.006
The Genome Aggregation DatabaseEuropeSub18464G=0.765A=0.234
The Genome Aggregation DatabaseGlobalStudy-wide29932G=0.657A=0.342
The Genome Aggregation DatabaseOtherSub302G=0.850A=0.150
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.591A=0.408
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.773A=0.227
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs6196724.59E-05alcohol and nictotine co-dependence20158304

eQTL of rs619672 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 rs619672 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 )
chr741691184169369E068-26619
chr741695684169705E068-26283
chr742295684230056E06833580
chr741691184169369E069-26619
chr741695684169705E069-26283
chr741698744169927E069-26061
chr741699944170034E069-25954
chr742284914229225E06932503
chr741695684169705E070-26283
chr741698744169927E070-26061
chr741699944170034E070-25954
chr741702834170544E070-25444
chr741764634176517E070-19471
chr741766794176741E070-19247
chr741771164177166E070-18822
chr741772474177328E070-18660
chr741773834177491E070-18497
chr741851494185485E070-10503
chr741877334187853E070-8135
chr741878564187906E070-8082
chr742284914229225E07032503
chr742295684230056E07033580
chr742301744230272E07034186
chr742302934230471E07034305
chr742306844230724E07034696
chr741691184169369E071-26619
chr741695684169705E071-26283
chr742284914229225E07132503
chr741695684169705E072-26283
chr741691184169369E073-26619
chr741695684169705E073-26283
chr742032904203385E0737302
chr741691184169369E074-26619
chr741695684169705E074-26283
chr742284914229225E07432503
chr741675174167577E081-28411
chr741675994167823E081-28165
chr741732784173388E081-22600
chr741752584175488E081-20500
chr741755314175598E081-20390
chr741756124176419E081-19569
chr741764634176517E081-19471
chr741777714178062E081-17926
chr741794924180427E081-15561
chr741834684183651E081-12337
chr741836934184104E081-11884
chr741841254185110E081-10878
chr741851494185485E081-10503
chr742284914229225E08132503
chr742295684230056E08133580
chr742301744230272E08134186
chr742302934230471E08134305
chr742306844230724E08134696
chr742308654231020E08134877
chr742312654231315E08135277
chr742313534231433E08135365
chr742315164231674E08135528
chr742317234231967E08135735
chr742425194242631E08146531
chr742428154242997E08146827
chr742430894243139E08147101
chr742432044243541E08147216
chr742437984243906E08147810
chr742439544244412E08147966
chr741752584175488E082-20500
chr742295684230056E08233580
chr742301744230272E08234186
chr742302934230471E08234305
chr742432044243541E08247216
chr742437984243906E08247810









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr742444304244671E07048442