rs2979062

Homo sapiens
T>C
XKR4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0182 (5448/29942,GnomAD)
C=0259 (7555/29118,TOPMED)
C=0189 (946/5008,1000G)
C=0058 (223/3854,ALSPAC)
C=0064 (238/3708,TWINSUK)
chr8:55402359 (GRCh38.p7) (8q12.1)
ND
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.55402359T>C
GRCh37.p13 chr 8NC_000008.10:g.56314919T>C

Gene: XKR4, XK related 4(plus strand)

Molecule type Change Amino acid[Codon] SO Term
XKR4 transcriptNM_052898.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.443C=0.557
1000GenomesAmericanSub694T=0.910C=0.090
1000GenomesEast AsianSub1008T=0.997C=0.003
1000GenomesEuropeSub1006T=0.944C=0.056
1000GenomesGlobalStudy-wide5008T=0.811C=0.189
1000GenomesSouth AsianSub978T=0.910C=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.942C=0.058
The Genome Aggregation DatabaseAfricanSub8696T=0.499C=0.501
The Genome Aggregation DatabaseAmericanSub838T=0.930C=0.070
The Genome Aggregation DatabaseEast AsianSub1622T=0.992C=0.008
The Genome Aggregation DatabaseEuropeSub18484T=0.945C=0.054
The Genome Aggregation DatabaseGlobalStudy-wide29942T=0.818C=0.182
The Genome Aggregation DatabaseOtherSub302T=0.920C=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.740C=0.259
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.936C=0.064
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs29790620.000708nicotine smoking19268276

eQTL of rs2979062 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 rs2979062 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 )
chr85631790156317968E0672982
chr85632503156325105E06810112
chr85632503156325105E06910112
chr85632266256322900E0707743
chr85632348956323539E0818570
chr85633640256336739E08121483
chr85633679856336939E08121879
chr85636048256360683E08145563
chr85636085256361139E08145933