rs1286665

Homo sapiens
C>T
RARB : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0396 (11846/29910,GnomAD)
T=0451 (13150/29118,TOPMED)
T=0423 (2117/5008,1000G)
T=0287 (1106/3854,ALSPAC)
T=0270 (1001/3708,TWINSUK)
chr3:25534184 (GRCh38.p7) (3p24.2)
AD
GWASdb2
1   publication(s)
See rs on genome
57 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.25534184C>T
GRCh37.p13 chr 3NC_000003.11:g.25575675C>T
RARB RefSeqGeneNG_029013.2:g.364853C>T

Gene: RARB, retinoic acid receptor beta(plus strand)

Molecule type Change Amino acid[Codon] SO Term
RARB transcript variant 1NM_000965.4:c.N/AIntron Variant
RARB transcript variant 3NM_001290216.2:c.N/AIntron Variant
RARB transcript variant 4NM_001290217.1:c.N/AIntron Variant
RARB transcript variant 2NM_001290266.1:c.N/AIntron Variant
RARB transcript variant 1NM_001290276.1:c.N/AIntron Variant
RARB transcript variant 5NM_001290277.1:c.N/AIntron Variant
RARB transcript variant 8NM_001290300.1:c.N/AIntron Variant
RARB transcript variant 2NM_016152.3:c.N/AIntron Variant
RARB transcript variant 6NR_110892.1:n.N/AIntron Variant
RARB transcript variant 7NR_110893.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.289T=0.711
1000GenomesAmericanSub694C=0.670T=0.330
1000GenomesEast AsianSub1008C=0.610T=0.390
1000GenomesEuropeSub1006C=0.726T=0.274
1000GenomesGlobalStudy-wide5008C=0.577T=0.423
1000GenomesSouth AsianSub978C=0.710T=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.713T=0.287
The Genome Aggregation DatabaseAfricanSub8698C=0.341T=0.659
The Genome Aggregation DatabaseAmericanSub834C=0.650T=0.350
The Genome Aggregation DatabaseEast AsianSub1604C=0.617T=0.383
The Genome Aggregation DatabaseEuropeSub18474C=0.724T=0.275
The Genome Aggregation DatabaseGlobalStudy-wide29910C=0.603T=0.396
The Genome Aggregation DatabaseOtherSub300C=0.630T=0.370
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.548T=0.451
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.730T=0.270
PMID Title Author Journal
22072270Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms.Wang KSJ Neural Transm (Vienna)

P-Value

SNP ID p-value Traits Study
rs12866654.34E-05alcohol withdrawal symptoms22072270

eQTL of rs1286665 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 rs1286665 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 )
chr32554024925540794E067-34881
chr32554539625545816E067-29859
chr32555089425551032E067-24643
chr32555123225551282E067-24393
chr32555496825555115E067-20560
chr32556869325568796E067-6879
chr32556891625569270E067-6405
chr32556943625569756E067-5919
chr32554518525545298E068-30377
chr32554539625545816E068-29859
chr32554590925545959E068-29716
chr32554931325549883E068-25792
chr32554992525549975E068-25700
chr32555496825555115E068-20560
chr32555518525555759E068-19916
chr32556943625569756E068-5919
chr32558039225580763E0684717
chr32558093625581008E0685261
chr32559905225599123E06823377
chr32559920525599500E06823530
chr32560010025600147E06824425
chr32554024925540794E069-34881
chr32554539625545816E069-29859
chr32556891625569270E069-6405
chr32556943625569756E069-5919
chr32554539625545816E070-29859
chr32554590925545959E070-29716
chr32555518525555759E070-19916
chr32556943625569756E070-5919
chr32554539625545816E071-29859
chr32554590925545959E071-29716
chr32555518525555759E071-19916
chr32559905225599123E07123377
chr32559920525599500E07123530
chr32554539625545816E072-29859
chr32554590925545959E072-29716
chr32555029425550858E072-24817
chr32555089425551032E072-24643
chr32555108425551134E072-24541
chr32555123225551282E072-24393
chr32556943625569756E072-5919
chr32561000525610068E07234330
chr32553996025540031E073-35644
chr32554009225540166E073-35509
chr32554024925540794E073-34881
chr32554518525545298E073-30377
chr32554539625545816E073-29859
chr32555404925554115E073-21560
chr32561420325614864E07338528
chr32561486725615384E07339192
chr32561545025615575E07339775
chr32561559925615697E07339924
chr32554518525545298E074-30377
chr32554539625545816E074-29859
chr32554590925545959E074-29716
chr32552723925527411E081-48264
chr32561486725615384E08139192