rs630379

Homo sapiens
A>C
NELFE : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0225 (25906/114970,ExAC)
A==0231 (6909/29914,GnomAD)
A==0177 (5154/29118,TOPMED)
C=0220 (2871/13006,GO-ESP)
A==0165 (826/5008,1000G)
A==0311 (1199/3854,ALSPAC)
A==0318 (1180/3708,TWINSUK)
chr6:31954477 (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.31954477A>C
GRCh37.p13 chr 6NC_000006.11:g.31922254A>C
SKIV2L RefSeqGeneNG_032652.1:g.674A>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.3431904A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.3432010A>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.3255666C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.3254964C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.3296513C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.3302098C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.3210452C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.3216048C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.3202257C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.3207842C>A

Gene: NELFE, negative elongation factor complex member E(minus strand)

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

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.064C=0.936
1000GenomesAmericanSub694A=0.240C=0.760
1000GenomesEast AsianSub1008A=0.295C=0.705
1000GenomesEuropeSub1006A=0.213C=0.787
1000GenomesGlobalStudy-wide5008A=0.165C=0.835
1000GenomesSouth AsianSub978A=0.060C=0.940
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.311C=0.689
The Exome Aggregation ConsortiumAmericanSub21832A=0.176C=0.823
The Exome Aggregation ConsortiumAsianSub20666A=0.153C=0.846
The Exome Aggregation ConsortiumEuropeSub71624A=0.261C=0.738
The Exome Aggregation ConsortiumGlobalStudy-wide114970A=0.225C=0.774
The Exome Aggregation ConsortiumOtherSub848A=0.180C=0.820
The Genome Aggregation DatabaseAfricanSub8714A=0.096C=0.904
The Genome Aggregation DatabaseAmericanSub834A=0.240C=0.760
The Genome Aggregation DatabaseEast AsianSub1616A=0.296C=0.704
The Genome Aggregation DatabaseEuropeSub18448A=0.290C=0.709
The Genome Aggregation DatabaseGlobalStudy-wide29914A=0.231C=0.769
The Genome Aggregation DatabaseOtherSub302A=0.110C=0.890
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.177C=0.823
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.318C=0.682
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
rs6303790.00023Alcohol dependence (early age of onset)20201924
rs6303790.00062alcohol dependence20201924

eQTL of rs630379 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:31922254HLA-CENSG00000204525.10A>C8.5000e-26682372Cerebellum
Chr6:31922254XXbac-BPG248L24.12ENSG00000271581.1A>C1.7316e-22597830Cerebellum
Chr6:31922254CYP21A1PENSG00000204338.4A>C1.1355e-10-51212Cerebellum
Chr6:31922254HLA-CENSG00000204525.10A>C3.2336e-20682372Cortex
Chr6:31922254CYP21A1PENSG00000204338.4A>C9.0047e-8-51212Cortex
Chr6:31922254HLA-DRB1ENSG00000196126.6A>C3.9457e-10-635371Cortex
Chr6:31922254HLA-CENSG00000204525.10A>C4.3410e-25682372Cerebellar_Hemisphere
Chr6:31922254WASF5PENSG00000231402.1A>C1.7109e-5665513Cerebellar_Hemisphere
Chr6:31922254CYP21A1PENSG00000204338.4A>C3.5262e-8-51212Caudate_basal_ganglia
Chr6:31922254HLA-DRB5ENSG00000198502.5A>C2.1350e-25-575810Caudate_basal_ganglia
Chr6:31922254CYP21A1PENSG00000204338.4A>C2.1327e-6-51212Anterior_cingulate_cortex
Chr6:31922254HLA-DRB1ENSG00000196126.6A>C2.2973e-5-635371Nucleus_accumbens_basal_ganglia

meQTL of rs630379 in Fetal Brain

Probe ID Position Gene beta p-value
cg20544437chr6:31839329SLC44A40.05039668506372174.8346e-10
cg18020334chr6:31239243HLA-C-0.07362803598383279.1991e-10
cg15454374chr6:31325455HLA-B-0.07183397633026887.9006e-9

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 )
chr63192570831925758E0673454
chr63193784631938426E06715592
chr63192570831925758E0683454
chr63193784631938426E06815592
chr63192570831925758E0693454
chr63193784631938426E06915592
chr63192570831925758E0703454
chr63191287331912941E071-9313
chr63192570831925758E0713454
chr63193784631938426E07115592
chr63193752231937627E07215268
chr63193766031937734E07215406
chr63193784631938426E07215592
chr63194166831941767E07219414
chr63191287331912941E073-9313
chr63192457531924646E0732321
chr63192570831925758E0733454
chr63193723131937313E07314977
chr63193752231937627E07315268
chr63192570831925758E0743454
chr63192570831925758E0813454
chr63193784631938426E08115592
chr63194166831941767E08119414
chr63193723131937313E08214977
chr63193752231937627E08215268
chr63193766031937734E08215406










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63192627931927462E0674025
chr63193849231941215E06716238
chr63189537931895518E068-26736
chr63189564231895736E068-26518
chr63192627931927462E0684025
chr63193849231941215E06816238
chr63192627931927462E0694025
chr63193849231941215E06916238
chr63192627931927462E0704025
chr63193849231941215E07016238
chr63189564231895736E071-26518
chr63192627931927462E0714025
chr63193849231941215E07116238
chr63192627931927462E0724025
chr63193849231941215E07216238
chr63189537931895518E073-26736
chr63189564231895736E073-26518
chr63192627931927462E0734025
chr63193849231941215E07316238
chr63192627931927462E0744025
chr63193849231941215E07416238
chr63192627931927462E0814025
chr63193849231941215E08116238
chr63192627931927462E0824025
chr63193849231941215E08216238