rs13408416

Homo sapiens
C>T
COPS7B : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0020 (2163/107686,ExAC)
T=0025 (762/29936,GnomAD)
T=0036 (1052/29118,TOPMED)
C==0029 (377/13004,GO-ESP)
T=0038 (188/5008,1000G)
T=0003 (12/3854,ALSPAC)
T=0003 (12/3708,TWINSUK)
chr2:231796358 (GRCh38.p7) (2q37.1)
AD
GWASdb2
1   publication(s)
See rs on genome
67 Enhancers around
38 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.231796358C>T
GRCh37.p13 chr 2NC_000002.11:g.232661068C>T

Gene: COPS7B, COP9 signalosome subunit 7B(plus strand)

Molecule type Change Amino acid[Codon] SO Term
COPS7B transcript variant 3NM_001282949.2:c.N/AIntron Variant
COPS7B transcript variant 1NM_001282950.2:c.N/AIntron Variant
COPS7B transcript variant 4NM_001282951.2:c.N/AIntron Variant
COPS7B transcript variant 5NM_001282952.2:c.N/AIntron Variant
COPS7B transcript variant 6NM_001308381.1:c.N/AIntron Variant
COPS7B transcript variant 2NM_022730.3:c.N/AIntron Variant
COPS7B transcript variant X1XM_006712693.1:c.N/AIntron Variant
COPS7B transcript variant X4XM_011511638.1:c.N/AIntron Variant
COPS7B transcript variant X5XM_011511639.1:c.N/AIntron Variant
COPS7B transcript variant X6XM_011511640.1:c.N/AIntron Variant
COPS7B transcript variant X2XM_017004716.1:c.N/AIntron Variant
COPS7B transcript variant X8XM_017004717.1:c.N/AIntron Variant
COPS7B transcript variant X3XR_001738900.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.903T=0.097
1000GenomesAmericanSub694C=0.990T=0.010
1000GenomesEast AsianSub1008C=0.998T=0.002
1000GenomesEuropeSub1006C=0.992T=0.008
1000GenomesGlobalStudy-wide5008C=0.962T=0.038
1000GenomesSouth AsianSub978C=0.960T=0.040
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.997T=0.003
The Exome Aggregation ConsortiumAmericanSub18848C=0.955T=0.044
The Exome Aggregation ConsortiumAsianSub22406C=0.964T=0.035
The Exome Aggregation ConsortiumEuropeSub65622C=0.992T=0.007
The Exome Aggregation ConsortiumGlobalStudy-wide107686C=0.979T=0.020
The Exome Aggregation ConsortiumOtherSub810C=0.970T=0.030
The Genome Aggregation DatabaseAfricanSub8714C=0.924T=0.076
The Genome Aggregation DatabaseAmericanSub838C=0.990T=0.010
The Genome Aggregation DatabaseEast AsianSub1622C=0.999T=0.001
The Genome Aggregation DatabaseEuropeSub18460C=0.995T=0.004
The Genome Aggregation DatabaseGlobalStudy-wide29936C=0.974T=0.025
The Genome Aggregation DatabaseOtherSub302C=1.000T=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.963T=0.036
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.997T=0.003
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
rs134084160.000974alcohol dependence20201924

eQTL of rs13408416 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs13408416 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 )
chr2232629315232629375E067-31693
chr2232629601232629810E067-31258
chr2232629897232629956E067-31112
chr2232630292232630541E067-30527
chr2232644661232644719E067-16349
chr2232649358232649398E067-11670
chr2232652308232652348E067-8720
chr2232652617232652688E067-8380
chr2232657631232657819E067-3249
chr2232658534232658589E067-2479
chr2232629315232629375E068-31693
chr2232629601232629810E068-31258
chr2232629897232629956E068-31112
chr2232630292232630541E068-30527
chr2232631223232631267E068-29801
chr2232649358232649398E068-11670
chr2232649945232650009E068-11059
chr2232652617232652688E068-8380
chr2232653747232653791E068-7277
chr2232657631232657819E068-3249
chr2232629315232629375E069-31693
chr2232629601232629810E069-31258
chr2232629897232629956E069-31112
chr2232630292232630541E069-30527
chr2232644661232644719E069-16349
chr2232649945232650009E069-11059
chr2232652308232652348E069-8720
chr2232657631232657819E069-3249
chr2232629601232629810E070-31258
chr2232629897232629956E070-31112
chr2232630292232630541E070-30527
chr2232629315232629375E071-31693
chr2232629601232629810E071-31258
chr2232629897232629956E071-31112
chr2232630292232630541E071-30527
chr2232631223232631267E071-29801
chr2232644661232644719E071-16349
chr2232649358232649398E071-11670
chr2232649945232650009E071-11059
chr2232652308232652348E071-8720
chr2232629315232629375E072-31693
chr2232629601232629810E072-31258
chr2232629897232629956E072-31112
chr2232630292232630541E072-30527
chr2232631223232631267E072-29801
chr2232657631232657819E072-3249
chr2232629315232629375E073-31693
chr2232629601232629810E073-31258
chr2232629897232629956E073-31112
chr2232630292232630541E073-30527
chr2232644661232644719E073-16349
chr2232652308232652348E073-8720
chr2232652617232652688E073-8380
chr2232653747232653791E073-7277
chr2232655943232656224E073-4844
chr2232629315232629375E074-31693
chr2232629601232629810E074-31258
chr2232629897232629956E074-31112
chr2232630292232630541E074-30527
chr2232631223232631267E074-29801
chr2232644661232644719E074-16349
chr2232649358232649398E074-11670
chr2232652308232652348E074-8720
chr2232652617232652688E074-8380
chr2232644661232644719E081-16349
chr2232652617232652688E081-8380
chr2232652308232652348E082-8720










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2232645317232645433E067-15635
chr2232645435232645515E067-15553
chr2232645526232647349E067-13719
chr2232650578232651774E067-9294
chr2232645317232645433E068-15635
chr2232645435232645515E068-15553
chr2232645526232647349E068-13719
chr2232650578232651774E068-9294
chr2232645317232645433E069-15635
chr2232645435232645515E069-15553
chr2232645526232647349E069-13719
chr2232650578232651774E069-9294
chr2232645317232645433E070-15635
chr2232645435232645515E070-15553
chr2232645526232647349E070-13719
chr2232650578232651774E070-9294
chr2232645317232645433E071-15635
chr2232645435232645515E071-15553
chr2232645526232647349E071-13719
chr2232650578232651774E071-9294
chr2232645317232645433E072-15635
chr2232645435232645515E072-15553
chr2232645526232647349E072-13719
chr2232650578232651774E072-9294
chr2232645317232645433E073-15635
chr2232645435232645515E073-15553
chr2232645526232647349E073-13719
chr2232650578232651774E073-9294
chr2232645317232645433E074-15635
chr2232645435232645515E074-15553
chr2232645526232647349E074-13719
chr2232650578232651774E074-9294
chr2232645526232647349E081-13719
chr2232650578232651774E081-9294
chr2232645317232645433E082-15635
chr2232645435232645515E082-15553
chr2232645526232647349E082-13719
chr2232650578232651774E082-9294