rs3777599

Homo sapiens
G>T
CLIC5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0331 (9902/29904,GnomAD)
T=0302 (8802/29118,TOPMED)
T=0261 (1307/5008,1000G)
T=0287 (1107/3854,ALSPAC)
T=0289 (1071/3708,TWINSUK)
chr6:45975213 (GRCh38.p7) (6p21.1)
ND
GWASdb2
1   publication(s)
See rs on genome
8 Enhancers around
13 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.45975213G>T
GRCh37.p13 chr 6NC_000006.11:g.45942950G>T
CLIC5 RefSeqGeneNG_031965.1:g.110136C>A

Gene: CLIC5, chloride intracellular channel 5(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CLIC5 transcript variant 1NM_001114086.1:c.N/AIntron Variant
CLIC5 transcript variant 3NM_001256023.1:c.N/AIntron Variant
CLIC5 transcript variant 2NM_016929.4:c.N/AIntron Variant
CLIC5 transcript variant 4NR_045672.1:n.N/AGenic Upstream Transcript Variant
CLIC5 transcript variant 5NR_045673.1:n.N/AGenic Upstream Transcript Variant
CLIC5 transcript variant 6NR_045674.1:n.N/AGenic Upstream Transcript Variant
CLIC5 transcript variant X3XM_011514692.2:c.N/AIntron Variant
CLIC5 transcript variant X4XM_011514694.2:c.N/AIntron Variant
CLIC5 transcript variant X1XM_017010953.1:c.N/AIntron Variant
CLIC5 transcript variant X2XR_926258.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.628T=0.372
1000GenomesAmericanSub694G=0.650T=0.350
1000GenomesEast AsianSub1008G=0.910T=0.090
1000GenomesEuropeSub1006G=0.686T=0.314
1000GenomesGlobalStudy-wide5008G=0.739T=0.261
1000GenomesSouth AsianSub978G=0.830T=0.170
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.713T=0.287
The Genome Aggregation DatabaseAfricanSub8692G=0.656T=0.344
The Genome Aggregation DatabaseAmericanSub838G=0.580T=0.420
The Genome Aggregation DatabaseEast AsianSub1618G=0.933T=0.067
The Genome Aggregation DatabaseEuropeSub18454G=0.655T=0.344
The Genome Aggregation DatabaseGlobalStudy-wide29904G=0.668T=0.331
The Genome Aggregation DatabaseOtherSub302G=0.670T=0.330
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.697T=0.302
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.711T=0.289
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs37775995.7E-05alcohol and nictotine co-dependence20158304

eQTL of rs3777599 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 rs3777599 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 )
chr64589809145898599E070-44351
chr64591916145919295E070-23655
chr64591938145919820E070-23130
chr64589809145898599E072-44351
chr64591916145919295E072-23655
chr64591938145919820E072-23130
chr64589809145898599E074-44351
chr64589860145898734E074-44216



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr64598279045983673E06739840
chr64598372445983831E06740774
chr64598178845982743E06838838
chr64598279045983673E06839840
chr64598372445983831E06840774
chr64598279045983673E06939840
chr64598372445983831E06940774
chr64598372445983831E07140774
chr64598397445984136E07141024
chr64598279045983673E07239840
chr64598279045983673E07339840
chr64598372445983831E07340774
chr64598279045983673E07439840