rs419788

Homo sapiens
T>C
SKIV2L : Intron VariantNELFE : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0230 (27074/117514,ExAC)
T==0234 (7020/29916,GnomAD)
T==0181 (5287/29118,TOPMED)
C=0223 (1883/8440,GO-ESP)
T==0184 (920/5008,1000G)
T==0314 (1210/3854,ALSPAC)
T==0322 (1195/3708,TWINSUK)
chr6:31961022 (GRCh38.p7) (6p21.33)
AD
GWASdb2
7   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.31961022T>C
GRCh37.p13 chr 6NC_000006.11:g.31928799T>C
SKIV2L RefSeqGeneNG_032652.1:g.7219T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.3438449T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.3438555T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.3262211C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.3261509C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.3303058C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.3308643C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.3216992C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.3222588C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.3208797C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.3214382C>T

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

Molecule type Change Amino acid[Codon] SO Term
SKIV2L transcriptNM_006929.4:c.N/AIntron Variant
SKIV2L transcript variant X1XM_011514815.2:c.N/AIntron Variant
SKIV2L transcript variant X2XR_001743586.1:n.N/AIntron Variant
SKIV2L transcript variant X3XR_926301.2:n.N/AIntron Variant

Gene: NELFE, negative elongation factor complex member E(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
NELFE transcriptNM_002904.5:c.N/AUpstream Transcript Variant
NELFE transcript variant X1XM_006715205.3:c.N/AN/A
NELFE transcript variant X2XM_011514913.2:c.N/AN/A
NELFE transcript variant X3XM_017011299.1:c.N/AN/A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.064C=0.936
1000GenomesAmericanSub694T=0.250C=0.750
1000GenomesEast AsianSub1008T=0.325C=0.675
1000GenomesEuropeSub1006T=0.217C=0.783
1000GenomesGlobalStudy-wide5008T=0.184C=0.816
1000GenomesSouth AsianSub978T=0.120C=0.880
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.314C=0.686
The Exome Aggregation ConsortiumAmericanSub20970T=0.184C=0.815
The Exome Aggregation ConsortiumAsianSub25038T=0.167C=0.832
The Exome Aggregation ConsortiumEuropeSub70616T=0.266C=0.733
The Exome Aggregation ConsortiumGlobalStudy-wide117514T=0.230C=0.769
The Exome Aggregation ConsortiumOtherSub890T=0.200C=0.800
The Genome Aggregation DatabaseAfricanSub8714T=0.098C=0.902
The Genome Aggregation DatabaseAmericanSub834T=0.250C=0.750
The Genome Aggregation DatabaseEast AsianSub1614T=0.302C=0.698
The Genome Aggregation DatabaseEuropeSub18452T=0.294C=0.705
The Genome Aggregation DatabaseGlobalStudy-wide29916T=0.234C=0.765
The Genome Aggregation DatabaseOtherSub302T=0.130C=0.870
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.181C=0.818
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.322C=0.678
PMID Title Author Journal
28449694The MHC locus and genetic susceptibility to autoimmune and infectious diseases.Matzaraki VGenome Biol
22170232Amino acid position 11 of HLA-DRbeta1 is a major determinant of chromosome 6p association with ulcerative colitis.Achkar JPGenes Immun
28056976A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients.Paziewska ABMC Med Genomics
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
19851445High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.Barcellos LFPLoS Genet
22761632Role of MHC-linked susceptibility genes in the pathogenesis of human and murine lupus.Relle MClin Dev Immunol
17997607Identification of two independent risk factors for lupus within the MHC in United Kingdom families.Fernando MMPLoS Genet

P-Value

SNP ID p-value Traits Study
rs4197880.00033alcohol dependence(early age of onset)20201924
rs4197880.00096alcohol dependence20201924

eQTL of rs419788 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:31928799HLA-CENSG00000204525.10T>C8.5000e-26688917Cerebellum
Chr6:31928799XXbac-BPG248L24.12ENSG00000271581.1T>C1.7316e-22604375Cerebellum
Chr6:31928799SKIV2LENSG00000204351.7T>C9.5905e-221911Cerebellum
Chr6:31928799CYP21A1PENSG00000204338.4T>C1.1355e-10-44667Cerebellum
Chr6:31928799CYP21A1PENSG00000204338.4T>C9.0047e-8-44667Cortex
Chr6:31928799HLA-DRB1ENSG00000196126.6T>C3.9457e-10-628826Cortex
Chr6:31928799HLA-CENSG00000204525.10T>C4.3410e-25688917Cerebellar_Hemisphere
Chr6:31928799WASF5PENSG00000231402.1T>C1.7109e-5672058Cerebellar_Hemisphere
Chr6:31928799CYP21A1PENSG00000204338.4T>C3.5262e-8-44667Caudate_basal_ganglia
Chr6:31928799HLA-DRB5ENSG00000198502.5T>C2.1350e-25-569265Caudate_basal_ganglia
Chr6:31928799CYP21A1PENSG00000204338.4T>C3.6100e-4-44667Brain_Spinal_cord_cervical
Chr6:31928799CYP21A1PENSG00000204338.4T>C2.1327e-6-44667Anterior_cingulate_cortex
Chr6:31928799HLA-DRB1ENSG00000196126.6T>C2.2973e-5-628826Nucleus_accumbens_basal_ganglia

meQTL of rs419788 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 )
chr63192570831925758E067-3041
chr63193784631938426E0679047
chr63192570831925758E068-3041
chr63193784631938426E0689047
chr63192570831925758E069-3041
chr63193784631938426E0699047
chr63192570831925758E070-3041
chr63191287331912941E071-15858
chr63192570831925758E071-3041
chr63193784631938426E0719047
chr63193752231937627E0728723
chr63193766031937734E0728861
chr63193784631938426E0729047
chr63194166831941767E07212869
chr63191287331912941E073-15858
chr63192457531924646E073-4153
chr63192570831925758E073-3041
chr63193723131937313E0738432
chr63193752231937627E0738723
chr63192570831925758E074-3041
chr63192570831925758E081-3041
chr63193784631938426E0819047
chr63194166831941767E08112869
chr63193723131937313E0828432
chr63193752231937627E0828723
chr63193766031937734E0828861










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63192627931927462E067-1337
chr63193849231941215E0679693
chr63189537931895518E068-33281
chr63189564231895736E068-33063
chr63192627931927462E068-1337
chr63193849231941215E0689693
chr63192627931927462E069-1337
chr63193849231941215E0699693
chr63192627931927462E070-1337
chr63193849231941215E0709693
chr63189564231895736E071-33063
chr63192627931927462E071-1337
chr63193849231941215E0719693
chr63192627931927462E072-1337
chr63193849231941215E0729693
chr63189537931895518E073-33281
chr63189564231895736E073-33063
chr63192627931927462E073-1337
chr63193849231941215E0739693
chr63192627931927462E074-1337
chr63193849231941215E0749693
chr63192627931927462E081-1337
chr63193849231941215E0819693
chr63192627931927462E082-1337
chr63193849231941215E0829693