rs55828312

Homo sapiens
A>G
CHRNB3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0472 (13751/29118,TOPMED)
G=0377 (10126/26808,GnomAD)
G=0414 (2073/5008,1000G)
G=0219 (843/3854,ALSPAC)
G=0230 (851/3708,TWINSUK)
chr8:42734459 (GRCh38.p7) (8p11.21)
ND
GWASCatalog
1   publication(s)
See rs on genome
67 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.42734459A>G
GRCh37.p13 chr 8NC_000008.10:g.42589602A>G

Gene: CHRNB3, cholinergic receptor nicotinic beta 3 subunit(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CHRNB3 transcriptNM_000749.3:c.N/AIntron Variant
CHRNB3 transcript variant X1XM_011544390.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.126G=0.874
1000GenomesAmericanSub694A=0.700G=0.300
1000GenomesEast AsianSub1008A=0.785G=0.215
1000GenomesEuropeSub1006A=0.781G=0.219
1000GenomesGlobalStudy-wide5008A=0.586G=0.414
1000GenomesSouth AsianSub978A=0.720G=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.781G=0.219
The Genome Aggregation DatabaseAfricanSub7720A=0.231G=0.769
The Genome Aggregation DatabaseAmericanSub790A=0.750G=0.250
The Genome Aggregation DatabaseEast AsianSub1526A=0.807G=0.193
The Genome Aggregation DatabaseEuropeSub16490A=0.780G=0.219
The Genome Aggregation DatabaseGlobalStudy-wide26808A=0.622G=0.377
The Genome Aggregation DatabaseOtherSub282A=0.740G=0.260
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.527G=0.472
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.770G=0.230
PMID Title Author Journal
26440539Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence.Hancock DBTransl Psychiatry

P-Value

SNP ID p-value Traits Study
rs558283121E-06nicotine dependence26440539

eQTL of rs55828312 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 rs55828312 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 )
chr84255878642559348E067-30254
chr84255950742559557E067-30045
chr84255956442559738E067-29864
chr84255978342560036E067-29566
chr84261567442615724E06726072
chr84261576342615833E06726161
chr84261591442615998E06726312
chr84261602842616705E06726426
chr84261567442615724E06826072
chr84261576342615833E06826161
chr84261591442615998E06826312
chr84261602842616705E06826426
chr84261986842620110E06830266
chr84262020842620258E06830606
chr84262029642620496E06830694
chr84257551642576584E069-13018
chr84261567442615724E06926072
chr84261576342615833E06926161
chr84261591442615998E06926312
chr84261602842616705E06926426
chr84255878642559348E071-30254
chr84255950742559557E071-30045
chr84255956442559738E071-29864
chr84257551642576584E071-13018
chr84259581842596743E0716216
chr84259678542596841E0717183
chr84261567442615724E07126072
chr84261576342615833E07126161
chr84261591442615998E07126312
chr84261602842616705E07126426
chr84261986842620110E07130266
chr84262020842620258E07130606
chr84262029642620496E07130694
chr84254736742548251E072-41351
chr84257551642576584E072-13018
chr84259581842596743E0726216
chr84261567442615724E07226072
chr84261576342615833E07226161
chr84261591442615998E07226312
chr84261602842616705E07226426
chr84261986842620110E07230266
chr84262020842620258E07230606
chr84262029642620496E07230694
chr84257551642576584E073-13018
chr84261567442615724E07326072
chr84261576342615833E07326161
chr84261591442615998E07326312
chr84255878642559348E074-30254
chr84255950742559557E074-30045
chr84255956442559738E074-29864
chr84255978342560036E074-29566
chr84256031142560370E074-29232
chr84257551642576584E074-13018
chr84259678542596841E0747183
chr84259699542597311E0747393
chr84261539042615450E07425788
chr84261553442615594E07425932
chr84261567442615724E07426072
chr84261576342615833E07426161
chr84261591442615998E07426312
chr84261602842616705E07426426
chr84262020842620258E07430606
chr84262029642620496E07430694
chr84256031142560370E081-29232
chr84256054542560595E081-29007
chr84256060442560725E081-28877
chr84259699542597311E0817393