rs410851

Homo sapiens
T>C
SKIV2L : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0217 (25247/116136,ExAC)
T==0227 (6802/29888,GnomAD)
T==0169 (4929/29118,TOPMED)
C=0217 (1832/8434,GO-ESP)
T==0160 (803/5008,1000G)
T==0312 (1203/3854,ALSPAC)
T==0320 (1186/3708,TWINSUK)
chr6:31968891 (GRCh38.p7) (6p21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
26 Enhancers around
25 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.31968891T>C
GRCh37.p13 chr 6NC_000006.11:g.31936668T>C
SKIV2L RefSeqGeneNG_032652.1:g.15088T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.3446318T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.3446424T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.3270080C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.3269378C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.3310927C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.3316512C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.3224861C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.3230457C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.3216666C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.3222251C>T

Gene: SKIV2L, Ski2 like RNA helicase(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SKIV2L transcriptNM_006929.4:c.320...NM_006929.4:c.3201T>CY [TAT]> Y [TAC]Coding Sequence Variant
helicase SKI2WNP_008860.4:p.Tyr...NP_008860.4:p.Tyr1067=Y [Tyr]> Y [Tyr]Synonymous Variant
SKIV2L transcript variant X1XM_011514815.2:c.N/AGenic Downstream Transcript Variant
SKIV2L transcript variant X2XR_001743586.1:n....XR_001743586.1:n.3360T>CT>CNon Coding Transcript Variant
SKIV2L transcript variant X3XR_926301.2:n.327...XR_926301.2:n.3277T>CT>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.045C=0.955
1000GenomesAmericanSub694T=0.140C=0.860
1000GenomesEast AsianSub1008T=0.310C=0.690
1000GenomesEuropeSub1006T=0.216C=0.784
1000GenomesGlobalStudy-wide5008T=0.160C=0.840
1000GenomesSouth AsianSub978T=0.120C=0.880
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.312C=0.688
The Exome Aggregation ConsortiumAmericanSub20620T=0.114C=0.885
The Exome Aggregation ConsortiumAsianSub24746T=0.170C=0.829
The Exome Aggregation ConsortiumEuropeSub69900T=0.264C=0.735
The Exome Aggregation ConsortiumGlobalStudy-wide116136T=0.217C=0.782
The Exome Aggregation ConsortiumOtherSub870T=0.200C=0.800
The Genome Aggregation DatabaseAfricanSub8710T=0.085C=0.915
The Genome Aggregation DatabaseAmericanSub838T=0.160C=0.840
The Genome Aggregation DatabaseEast AsianSub1610T=0.318C=0.682
The Genome Aggregation DatabaseEuropeSub18428T=0.291C=0.708
The Genome Aggregation DatabaseGlobalStudy-wide29888T=0.227C=0.772
The Genome Aggregation DatabaseOtherSub302T=0.130C=0.870
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.169C=0.830
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.320C=0.680
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
rs4108510.00017alcohol dependence(early age of onset)20201924
rs4108510.00058alcohol dependence20201924

eQTL of rs410851 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:31936668HLA-CENSG00000204525.10T>C8.5000e-26696786Cerebellum
Chr6:31936668XXbac-BPG248L24.12ENSG00000271581.1T>C1.7316e-22612244Cerebellum
Chr6:31936668SKIV2LENSG00000204351.7T>C9.5905e-229780Cerebellum
Chr6:31936668CYP21A1PENSG00000204338.4T>C1.1355e-10-36798Cerebellum
Chr6:31936668CYP21A1PENSG00000204338.4T>C1.4139e-4-36798Frontal_Cortex_BA9
Chr6:31936668CYP21A1PENSG00000204338.4T>C9.0047e-8-36798Cortex
Chr6:31936668HLA-DRB1ENSG00000196126.6T>C3.9457e-10-620957Cortex
Chr6:31936668HLA-CENSG00000204525.10T>C4.3410e-25696786Cerebellar_Hemisphere
Chr6:31936668WASF5PENSG00000231402.1T>C1.7109e-5679927Cerebellar_Hemisphere
Chr6:31936668CYP21A1PENSG00000204338.4T>C2.2428e-7-36798Cerebellar_Hemisphere
Chr6:31936668CYP21A1PENSG00000204338.4T>C3.5262e-8-36798Caudate_basal_ganglia
Chr6:31936668HLA-DRB5ENSG00000198502.5T>C2.1350e-25-561396Caudate_basal_ganglia
Chr6:31936668CYP21A1PENSG00000204338.4T>C3.6100e-4-36798Brain_Spinal_cord_cervical
Chr6:31936668CYP21A1PENSG00000204338.4T>C2.1327e-6-36798Anterior_cingulate_cortex
Chr6:31936668CYP21A1PENSG00000204338.4T>C1.8655e-7-36798Amygdala

meQTL of rs410851 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 )
chr63192570831925758E067-10910
chr63193784631938426E0671178
chr63192570831925758E068-10910
chr63193784631938426E0681178
chr63192570831925758E069-10910
chr63193784631938426E0691178
chr63192570831925758E070-10910
chr63191287331912941E071-23727
chr63192570831925758E071-10910
chr63193784631938426E0711178
chr63193752231937627E072854
chr63193766031937734E072992
chr63193784631938426E0721178
chr63194166831941767E0725000
chr63191287331912941E073-23727
chr63192457531924646E073-12022
chr63192570831925758E073-10910
chr63193723131937313E073563
chr63193752231937627E073854
chr63192570831925758E074-10910
chr63192570831925758E081-10910
chr63193784631938426E0811178
chr63194166831941767E0815000
chr63193723131937313E082563
chr63193752231937627E082854
chr63193766031937734E082992










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63192627931927462E067-9206
chr63193849231941215E0671824
chr63189537931895518E068-41150
chr63189564231895736E068-40932
chr63192627931927462E068-9206
chr63193849231941215E0681824
chr63192627931927462E069-9206
chr63193849231941215E0691824
chr63192627931927462E070-9206
chr63193849231941215E0701824
chr63189564231895736E071-40932
chr63192627931927462E071-9206
chr63193849231941215E0711824
chr63192627931927462E072-9206
chr63193849231941215E0721824
chr63189537931895518E073-41150
chr63189564231895736E073-40932
chr63192627931927462E073-9206
chr63193849231941215E0731824
chr63192627931927462E074-9206
chr63193849231941215E0741824
chr63192627931927462E081-9206
chr63193849231941215E0811824
chr63192627931927462E082-9206
chr63193849231941215E0821824