rs1992864

Homo sapiens
C>T
SLC9A9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0417 (12450/29818,GnomAD)
T=0404 (11768/29118,TOPMED)
T=0479 (2401/5008,1000G)
T=0424 (1636/3854,ALSPAC)
T=0429 (1591/3708,TWINSUK)
chr3:143687600 (GRCh38.p7) (3q24)
ND
GWASdb2
1   publication(s)
See rs on genome
63 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.143687600C>T
GRCh37.p13 chr 3NC_000003.11:g.143406442C>T
SLC9A9 RefSeqGeneNG_017077.1:g.165932G>A

Gene: SLC9A9, solute carrier family 9 member A9(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC9A9 transcriptNM_173653.3:c.N/AIntron Variant
SLC9A9 transcript variant X3XM_011512703.2:c.N/AIntron Variant
SLC9A9 transcript variant X4XM_011512704.2:c.N/AIntron Variant
SLC9A9 transcript variant X1XM_017006202.1:c.N/AIntron Variant
SLC9A9 transcript variant X2XM_017006203.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.657T=0.343
1000GenomesAmericanSub694C=0.480T=0.520
1000GenomesEast AsianSub1008C=0.492T=0.508
1000GenomesEuropeSub1006C=0.570T=0.430
1000GenomesGlobalStudy-wide5008C=0.521T=0.479
1000GenomesSouth AsianSub978C=0.350T=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.576T=0.424
The Genome Aggregation DatabaseAfricanSub8674C=0.607T=0.393
The Genome Aggregation DatabaseAmericanSub832C=0.480T=0.520
The Genome Aggregation DatabaseEast AsianSub1598C=0.511T=0.489
The Genome Aggregation DatabaseEuropeSub18412C=0.582T=0.417
The Genome Aggregation DatabaseGlobalStudy-wide29818C=0.582T=0.417
The Genome Aggregation DatabaseOtherSub302C=0.540T=0.460
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.595T=0.404
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.571T=0.429
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
rs19928640.000748nicotine smoking19268276

eQTL of rs1992864 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 rs1992864 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 )
chr3143410224143410293E0673782
chr3143416955143417071E06710513
chr3143418311143418361E06711869
chr3143418400143418451E06711958
chr3143418616143418678E06712174
chr3143428426143428665E06721984
chr3143390612143390745E068-15697
chr3143392053143392131E068-14311
chr3143416955143417071E06810513
chr3143417671143417742E06811229
chr3143418311143418361E06811869
chr3143418400143418451E06811958
chr3143418616143418678E06812174
chr3143428426143428665E06821984
chr3143373817143374069E069-32373
chr3143390612143390745E069-15697
chr3143391324143391550E069-14892
chr3143392868143393683E069-12759
chr3143403317143403466E069-2976
chr3143416394143416462E0699952
chr3143416955143417071E06910513
chr3143417671143417742E06911229
chr3143418616143418678E06912174
chr3143426825143426904E06920383
chr3143428426143428665E06921984
chr3143391324143391550E070-14892
chr3143391739143391847E070-14595
chr3143392053143392131E070-14311
chr3143390612143390745E071-15697
chr3143417671143417742E07111229
chr3143418311143418361E07111869
chr3143418400143418451E07111958
chr3143418616143418678E07112174
chr3143450643143451140E07144201
chr3143451203143451243E07144761
chr3143403317143403466E072-2976
chr3143416955143417071E07210513
chr3143417671143417742E07211229
chr3143418311143418361E07211869
chr3143418400143418451E07211958
chr3143418616143418678E07212174
chr3143428426143428665E07221984
chr3143417671143417742E07311229
chr3143418311143418361E07311869
chr3143418400143418451E07311958
chr3143418616143418678E07312174
chr3143390612143390745E074-15697
chr3143391324143391550E074-14892
chr3143391739143391847E074-14595
chr3143410224143410293E0743782
chr3143416394143416462E0749952
chr3143416955143417071E07410513
chr3143417671143417742E07411229
chr3143418311143418361E07411869
chr3143418400143418451E07411958
chr3143418616143418678E07412174
chr3143428426143428665E07421984
chr3143450310143450443E07443868
chr3143450643143451140E07444201
chr3143446409143446530E08139967
chr3143450643143451140E08144201
chr3143451203143451243E08144761
chr3143450310143450443E08243868