rs2867709

Homo sapiens
C>A
C4orf22 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0406 (11840/29118,TOPMED)
C==0360 (10365/28726,GnomAD)
C==0431 (2156/5008,1000G)
C==0273 (1054/3854,ALSPAC)
C==0267 (991/3708,TWINSUK)
chr4:80329287 (GRCh38.p7) (4q21.21)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.80329287C>A
GRCh37.p13 chr 4NC_000004.11:g.81250441C>A

Gene: C4orf22, chromosome 4 open reading frame 22(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CFAP299 transcript variant 1NM_001206997.1:c.N/AGenic Upstream Transcript Variant
CFAP299 transcript variant 2NM_152770.2:c.N/AGenic Upstream Transcript Variant
CFAP299 transcript variant X8XM_011531816.2:c.N/AIntron Variant
CFAP299 transcript variant X1XM_017007972.1:c.N/AIntron Variant
CFAP299 transcript variant X2XM_017007973.1:c.N/AIntron Variant
CFAP299 transcript variant X3XM_017007974.1:c.N/AIntron Variant
CFAP299 transcript variant X5XM_017007976.1:c.N/AIntron Variant
CFAP299 transcript variant X6XM_017007977.1:c.N/AIntron Variant
CFAP299 transcript variant X4XM_017007975.1:c.N/AGenic Upstream Transcript Variant
CFAP299 transcript variant X7XM_017007978.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.583A=0.417
1000GenomesAmericanSub694C=0.350A=0.650
1000GenomesEast AsianSub1008C=0.351A=0.649
1000GenomesEuropeSub1006C=0.298A=0.702
1000GenomesGlobalStudy-wide5008C=0.431A=0.569
1000GenomesSouth AsianSub978C=0.500A=0.500
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.273A=0.727
The Genome Aggregation DatabaseAfricanSub8404C=0.542A=0.458
The Genome Aggregation DatabaseAmericanSub700C=0.360A=0.640
The Genome Aggregation DatabaseEast AsianSub1604C=0.367A=0.633
The Genome Aggregation DatabaseEuropeSub17718C=0.273A=0.726
The Genome Aggregation DatabaseGlobalStudy-wide28726C=0.360A=0.639
The Genome Aggregation DatabaseOtherSub300C=0.420A=0.580
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.406A=0.593
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.267A=0.733
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs28677099.1E-05alcoholism (heaviness of drinking)21529783

eQTL of rs2867709 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 rs2867709 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 )
chr48122905581229166E081-21275
chr48122828581228908E082-21533
chr48122905581229166E082-21275


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr48125657881257540E0676137
chr48125657881257540E0686137
chr48125657881257540E0696137
chr48125657881257540E0706137
chr48125657881257540E0716137
chr48125657881257540E0726137
chr48125657881257540E0746137
chr48125657881257540E0816137
chr48125657881257540E0826137