rs389883

Homo sapiens
G>T
STK19 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0229 (6835/29846,GnomAD)
G==0169 (4927/29118,TOPMED)
G==0161 (805/5008,1000G)
G==0312 (1202/3854,ALSPAC)
G==0321 (1189/3708,TWINSUK)
chr6:31979683 (GRCh38.p7) (6p21.33)
AD
GWASdb2
3   publication(s)
See rs on genome
26 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.31979683G>T
GRCh37.p13 chr 6NC_000006.11:g.31947460G>T
Rodgers blood group RefSeqGene LRG_137
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.3235654T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.3241250T>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.3227456T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.3233041T>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.3457110G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.3457216G>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.3280872T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.3280170T>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.3321720T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.3327305T>G

Gene: STK19, serine/threonine kinase 19(plus strand)

Molecule type Change Amino acid[Codon] SO Term
STK19 transcript variant 1NM_004197.1:c.N/AIntron Variant
STK19 transcript variant 2NM_032454.1:c.N/AIntron Variant
STK19 transcript variant 3NR_026717.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.046T=0.954
1000GenomesAmericanSub694G=0.140T=0.860
1000GenomesEast AsianSub1008G=0.311T=0.689
1000GenomesEuropeSub1006G=0.216T=0.784
1000GenomesGlobalStudy-wide5008G=0.161T=0.839
1000GenomesSouth AsianSub978G=0.120T=0.880
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.312T=0.688
The Genome Aggregation DatabaseAfricanSub8698G=0.085T=0.915
The Genome Aggregation DatabaseAmericanSub836G=0.160T=0.840
The Genome Aggregation DatabaseEast AsianSub1608G=0.315T=0.685
The Genome Aggregation DatabaseEuropeSub18402G=0.294T=0.705
The Genome Aggregation DatabaseGlobalStudy-wide29846G=0.229T=0.771
The Genome Aggregation DatabaseOtherSub302G=0.130T=0.870
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.169T=0.830
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.321T=0.679
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
20354563Linkage disequilibrium and age of HLA region SNPs in relation to classic HLA gene alleles within Europe.Evseeva IEur J Hum Genet
25075970The associations between immunity-related genes and breast cancer prognosis in Korean women.Choi JPLoS One

P-Value

SNP ID p-value Traits Study
rs3898830.00014alcohol dependence(early age of onset)20201924
rs3898830.00039alcohol dependence20201924

eQTL of rs389883 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:31947460HLA-CENSG00000204525.10G>T8.5000e-26707578Cerebellum
Chr6:31947460XXbac-BPG248L24.12ENSG00000271581.1G>T1.7316e-22623036Cerebellum
Chr6:31947460SKIV2LENSG00000204351.7G>T9.5905e-2220572Cerebellum
Chr6:31947460CYP21A1PENSG00000204338.4G>T1.1355e-10-26006Cerebellum
Chr6:31947460CYP21A1PENSG00000204338.4G>T1.4139e-4-26006Frontal_Cortex_BA9
Chr6:31947460CYP21A1PENSG00000204338.4G>T9.0047e-8-26006Cortex
Chr6:31947460HLA-DRB1ENSG00000196126.6G>T3.9457e-10-610165Cortex
Chr6:31947460HLA-CENSG00000204525.10G>T4.3410e-25707578Cerebellar_Hemisphere
Chr6:31947460WASF5PENSG00000231402.1G>T1.7109e-5690719Cerebellar_Hemisphere
Chr6:31947460CYP21A1PENSG00000204338.4G>T2.2428e-7-26006Cerebellar_Hemisphere
Chr6:31947460CYP21A1PENSG00000204338.4G>T3.5262e-8-26006Caudate_basal_ganglia
Chr6:31947460HLA-DRB5ENSG00000198502.5G>T2.1350e-25-550604Caudate_basal_ganglia
Chr6:31947460CYP21A1PENSG00000204338.4G>T3.6100e-4-26006Brain_Spinal_cord_cervical
Chr6:31947460CYP21A1PENSG00000204338.4G>T2.1327e-6-26006Anterior_cingulate_cortex
Chr6:31947460CYP21A1PENSG00000204338.4G>T1.8655e-7-26006Amygdala

meQTL of rs389883 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 )
chr63192570831925758E067-21702
chr63193784631938426E067-9034
chr63192570831925758E068-21702
chr63193784631938426E068-9034
chr63192570831925758E069-21702
chr63193784631938426E069-9034
chr63192570831925758E070-21702
chr63191287331912941E071-34519
chr63192570831925758E071-21702
chr63193784631938426E071-9034
chr63193752231937627E072-9833
chr63193766031937734E072-9726
chr63193784631938426E072-9034
chr63194166831941767E072-5693
chr63191287331912941E073-34519
chr63192457531924646E073-22814
chr63192570831925758E073-21702
chr63193723131937313E073-10147
chr63193752231937627E073-9833
chr63192570831925758E074-21702
chr63192570831925758E081-21702
chr63193784631938426E081-9034
chr63194166831941767E081-5693
chr63193723131937313E082-10147
chr63193752231937627E082-9833
chr63193766031937734E082-9726










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63192627931927462E067-19998
chr63193849231941215E067-6245
chr63192627931927462E068-19998
chr63193849231941215E068-6245
chr63192627931927462E069-19998
chr63193849231941215E069-6245
chr63192627931927462E070-19998
chr63193849231941215E070-6245
chr63192627931927462E071-19998
chr63193849231941215E071-6245
chr63192627931927462E072-19998
chr63193849231941215E072-6245
chr63192627931927462E073-19998
chr63193849231941215E073-6245
chr63192627931927462E074-19998
chr63193849231941215E074-6245
chr63192627931927462E081-19998
chr63193849231941215E081-6245
chr63192627931927462E082-19998
chr63193849231941215E082-6245