rs437179

Homo sapiens
A>C
SKIV2L : Missense Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0230 (27899/121272,ExAC)
A==0234 (7011/29904,GnomAD)
A==0181 (5285/29118,TOPMED)
C=0226 (2940/13006,GO-ESP)
A==0183 (918/5008,1000G)
A==0314 (1212/3854,ALSPAC)
A==0322 (1195/3708,TWINSUK)
chr6:31961237 (GRCh38.p7) (6p21.33)
AD
GWASdb2
3   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.31961237A>C
GRCh37.p13 chr 6NC_000006.11:g.31929014A>C
SKIV2L RefSeqGeneNG_032652.1:g.7434A>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.3438664A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.3438770A>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.3262426C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.3261724C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.3303273C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.3308858C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.3217207C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.3222803C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.3209012C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.3214597C>A

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

Molecule type Change Amino acid[Codon] SO Term
SKIV2L transcriptNM_006929.4:c.640A>CM [ATG]> L [CTG]Coding Sequence Variant
helicase SKI2WNP_008860.4:p.Met...NP_008860.4:p.Met214LeuM [Met]> L [Leu]Missense Variant
SKIV2L transcript variant X1XM_011514815.2:c....XM_011514815.2:c.640A>CM [ATG]> L [CTG]Coding Sequence Variant
helicase SKI2W isoform X1XP_011513117.1:p....XP_011513117.1:p.Met214LeuM [Met]> L [Leu]Missense Variant
SKIV2L transcript variant X2XR_001743586.1:n....XR_001743586.1:n.736A>CA>CNon Coding Transcript Variant
SKIV2L transcript variant X3XR_926301.2:n.736A>CA>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.064C=0.936
1000GenomesAmericanSub694A=0.250C=0.750
1000GenomesEast AsianSub1008A=0.324C=0.676
1000GenomesEuropeSub1006A=0.217C=0.783
1000GenomesGlobalStudy-wide5008A=0.183C=0.817
1000GenomesSouth AsianSub978A=0.120C=0.880
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.314C=0.686
The Exome Aggregation ConsortiumAmericanSub21958A=0.180C=0.819
The Exome Aggregation ConsortiumAsianSub25142A=0.168C=0.831
The Exome Aggregation ConsortiumEuropeSub73266A=0.266C=0.733
The Exome Aggregation ConsortiumGlobalStudy-wide121272A=0.230C=0.769
The Exome Aggregation ConsortiumOtherSub906A=0.210C=0.790
The Genome Aggregation DatabaseAfricanSub8702A=0.098C=0.902
The Genome Aggregation DatabaseAmericanSub838A=0.250C=0.750
The Genome Aggregation DatabaseEast AsianSub1616A=0.301C=0.699
The Genome Aggregation DatabaseEuropeSub18448A=0.294C=0.705
The Genome Aggregation DatabaseGlobalStudy-wide29904A=0.234C=0.765
The Genome Aggregation DatabaseOtherSub300A=0.120C=0.880
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.181C=0.818
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.322C=0.678
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
17486107A genome-wide association study implicates diacylglycerol kinase eta (DGKH) and several other genes in the etiology of bipolar disorder.Baum AEMol Psychiatry
27107574Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control study.Mullany LEBMC Med Genomics

P-Value

SNP ID p-value Traits Study
rs4371790.00035alcohol dependence20201924

eQTL of rs437179 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:31929014HLA-CENSG00000204525.10A>C8.5000e-26689132Cerebellum
Chr6:31929014XXbac-BPG248L24.12ENSG00000271581.1A>C1.7316e-22604590Cerebellum
Chr6:31929014SKIV2LENSG00000204351.7A>C9.5905e-222126Cerebellum
Chr6:31929014CYP21A1PENSG00000204338.4A>C1.1355e-10-44452Cerebellum
Chr6:31929014CYP21A1PENSG00000204338.4A>C9.0047e-8-44452Cortex
Chr6:31929014HLA-DRB1ENSG00000196126.6A>C3.9457e-10-628611Cortex
Chr6:31929014HLA-CENSG00000204525.10A>C4.3410e-25689132Cerebellar_Hemisphere
Chr6:31929014WASF5PENSG00000231402.1A>C1.7109e-5672273Cerebellar_Hemisphere
Chr6:31929014CYP21A1PENSG00000204338.4A>C3.5262e-8-44452Caudate_basal_ganglia
Chr6:31929014HLA-DRB5ENSG00000198502.5A>C2.1350e-25-569050Caudate_basal_ganglia
Chr6:31929014CYP21A1PENSG00000204338.4A>C3.6100e-4-44452Brain_Spinal_cord_cervical
Chr6:31929014CYP21A1PENSG00000204338.4A>C2.1327e-6-44452Anterior_cingulate_cortex
Chr6:31929014HLA-DRB1ENSG00000196126.6A>C2.2973e-5-628611Nucleus_accumbens_basal_ganglia

meQTL of rs437179 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 )
chr63192570831925758E067-3256
chr63193784631938426E0678832
chr63192570831925758E068-3256
chr63193784631938426E0688832
chr63192570831925758E069-3256
chr63193784631938426E0698832
chr63192570831925758E070-3256
chr63191287331912941E071-16073
chr63192570831925758E071-3256
chr63193784631938426E0718832
chr63193752231937627E0728508
chr63193766031937734E0728646
chr63193784631938426E0728832
chr63194166831941767E07212654
chr63191287331912941E073-16073
chr63192457531924646E073-4368
chr63192570831925758E073-3256
chr63193723131937313E0738217
chr63193752231937627E0738508
chr63192570831925758E074-3256
chr63192570831925758E081-3256
chr63193784631938426E0818832
chr63194166831941767E08112654
chr63193723131937313E0828217
chr63193752231937627E0828508
chr63193766031937734E0828646










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63192627931927462E067-1552
chr63193849231941215E0679478
chr63189537931895518E068-33496
chr63189564231895736E068-33278
chr63192627931927462E068-1552
chr63193849231941215E0689478
chr63192627931927462E069-1552
chr63193849231941215E0699478
chr63192627931927462E070-1552
chr63193849231941215E0709478
chr63189564231895736E071-33278
chr63192627931927462E071-1552
chr63193849231941215E0719478
chr63192627931927462E072-1552
chr63193849231941215E0729478
chr63189537931895518E073-33496
chr63189564231895736E073-33278
chr63192627931927462E073-1552
chr63193849231941215E0739478
chr63192627931927462E074-1552
chr63193849231941215E0749478
chr63192627931927462E081-1552
chr63193849231941215E0819478
chr63192627931927462E082-1552
chr63193849231941215E0829478