rs665648

Homo sapiens
G>A
CXCR5 : Missense Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0015 (1669/110012,ExAC)
A=0012 (373/29966,GnomAD)
A=0010 (291/29118,TOPMED)
G==0013 (180/12990,GO-ESP)
A=0008 (42/5008,1000G)
A=0021 (80/3854,ALSPAC)
A=0016 (59/3708,TWINSUK)
chr11:118894574 (GRCh38.p7) (11q23.3)
AD
GWASdb2
1   publication(s)
See rs on genome
71 Enhancers around
44 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.118894574G>A
GRCh37.p13 chr 11NC_000011.9:g.118765283G>A

Gene: CXCR5, chemokine (C-X-C motif) receptor 5(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CXCR5 transcript variant 1NM_001716.4:c.103...NM_001716.4:c.1030G>AG [GGC]> S [AGC]Coding Sequence Variant
C-X-C chemokine receptor type 5 isoform 1NP_001707.1:p.Gly...NP_001707.1:p.Gly344SerG [Gly]> S [Ser]Missense Variant
CXCR5 transcript variant 2NM_032966.2:c.895G>AG [GGC]> S [AGC]Coding Sequence Variant
C-X-C chemokine receptor type 5 isoform 2NP_116743.1:p.Gly...NP_116743.1:p.Gly299SerG [Gly]> S [Ser]Missense Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.998A=0.002
1000GenomesAmericanSub694G=0.990A=0.010
1000GenomesEast AsianSub1008G=1.000A=0.000
1000GenomesEuropeSub1006G=0.977A=0.023
1000GenomesGlobalStudy-wide5008G=0.992A=0.008
1000GenomesSouth AsianSub978G=0.990A=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.979A=0.021
The Exome Aggregation ConsortiumAmericanSub21554G=0.993A=0.006
The Exome Aggregation ConsortiumAsianSub17540G=0.994A=0.005
The Exome Aggregation ConsortiumEuropeSub70134G=0.979A=0.020
The Exome Aggregation ConsortiumGlobalStudy-wide110012G=0.984A=0.015
The Exome Aggregation ConsortiumOtherSub784G=0.980A=0.020
The Genome Aggregation DatabaseAfricanSub8728G=0.997A=0.003
The Genome Aggregation DatabaseAmericanSub838G=0.990A=0.010
The Genome Aggregation DatabaseEast AsianSub1622G=1.000A=0.000
The Genome Aggregation DatabaseEuropeSub18476G=0.982A=0.017
The Genome Aggregation DatabaseGlobalStudy-wide29966G=0.987A=0.012
The Genome Aggregation DatabaseOtherSub302G=0.960A=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.990A=0.010
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.984A=0.016
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
rs6656480.00068alcohol dependence20201924

eQTL of rs665648 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 rs665648 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 )
chr11118741858118742027E067-23256
chr11118759015118759147E067-6136
chr11118774247118774339E0678964
chr11118777473118779147E06712190
chr11118785648118785719E06720365
chr11118785771118786563E06720488
chr11118785648118785719E06820365
chr11118785771118786563E06820488
chr11118740375118740443E069-24840
chr11118767355118768067E0692072
chr11118777473118779147E06912190
chr11118785648118785719E06920365
chr11118785771118786563E06920488
chr11118809764118809814E06944481
chr11118809938118810536E06944655
chr11118810539118811450E06945256
chr11118777473118779147E07012190
chr11118785648118785719E07020365
chr11118785771118786563E07020488
chr11118809938118810536E07044655
chr11118810539118811450E07045256
chr11118740375118740443E071-24840
chr11118759015118759147E071-6136
chr11118759217118759449E071-5834
chr11118759584118759659E071-5624
chr11118759844118760123E071-5160
chr11118760124118760188E071-5095
chr11118777473118779147E07112190
chr11118785648118785719E07120365
chr11118785771118786563E07120488
chr11118740375118740443E072-24840
chr11118741858118742027E072-23256
chr11118777473118779147E07212190
chr11118785648118785719E07220365
chr11118785771118786563E07220488
chr11118809938118810536E07244655
chr11118810539118811450E07245256
chr11118811502118811626E07246219
chr11118811717118811770E07246434
chr11118767355118768067E0732072
chr11118777473118779147E07312190
chr11118785648118785719E07320365
chr11118785771118786563E07320488
chr11118809764118809814E07344481
chr11118809938118810536E07344655
chr11118810539118811450E07345256
chr11118811502118811626E07346219
chr11118740375118740443E074-24840
chr11118741858118742027E074-23256
chr11118759844118760123E074-5160
chr11118760124118760188E074-5095
chr11118777473118779147E07412190
chr11118785648118785719E07420365
chr11118785771118786563E07420488
chr11118777473118779147E08112190
chr11118785648118785719E08120365
chr11118785771118786563E08120488
chr11118809191118809756E08143908
chr11118809764118809814E08144481
chr11118809938118810536E08144655
chr11118810539118811450E08145256
chr11118811502118811626E08146219
chr11118768104118769010E0822821
chr11118777473118779147E08212190
chr11118785648118785719E08220365
chr11118785771118786563E08220488
chr11118809191118809756E08243908
chr11118809764118809814E08244481
chr11118811502118811626E08246219
chr11118811717118811770E08246434
chr11118811968118812018E08246685










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11118793838118796199E06728555
chr11118796220118796270E06730937
chr11118796358118796412E06731075
chr11118797487118801898E06732204
chr11118793838118796199E06828555
chr11118796220118796270E06830937
chr11118796358118796412E06831075
chr11118796437118797448E06831154
chr11118797487118801898E06832204
chr11118793838118796199E06928555
chr11118796220118796270E06930937
chr11118796358118796412E06931075
chr11118796437118797448E06931154
chr11118797487118801898E06932204
chr11118793838118796199E07028555
chr11118796220118796270E07030937
chr11118796358118796412E07031075
chr11118796437118797448E07031154
chr11118797487118801898E07032204
chr11118793838118796199E07128555
chr11118796220118796270E07130937
chr11118796358118796412E07131075
chr11118796437118797448E07131154
chr11118797487118801898E07132204
chr11118793838118796199E07228555
chr11118796220118796270E07230937
chr11118796358118796412E07231075
chr11118796437118797448E07231154
chr11118797487118801898E07232204
chr11118793838118796199E07328555
chr11118796220118796270E07330937
chr11118796358118796412E07331075
chr11118796437118797448E07331154
chr11118797487118801898E07332204
chr11118793838118796199E07428555
chr11118796220118796270E07430937
chr11118796358118796412E07431075
chr11118796437118797448E07431154
chr11118793838118796199E08128555
chr11118793838118796199E08228555
chr11118796220118796270E08230937
chr11118796358118796412E08231075
chr11118796437118797448E08231154
chr11118797487118801898E08232204