rs7639109

Homo sapiens
C>T
SLC9A9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0174 (5209/29934,GnomAD)
T=0249 (7260/29118,TOPMED)
T=0185 (926/5008,1000G)
T=0054 (210/3854,ALSPAC)
T=0054 (201/3708,TWINSUK)
chr3:143275352 (GRCh38.p7) (3q24)
AD
GWASdb2
1   publication(s)
See rs on genome
55 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.143275352C>T
GRCh37.p13 chr 3NC_000003.11:g.142994194C>T
SLC9A9 RefSeqGeneNG_017077.1:g.578180G>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 X2XM_017006203.1:c.N/AIntron Variant
SLC9A9 transcript variant X4XM_011512704.2:c.N/AGenic Downstream Transcript Variant
SLC9A9 transcript variant X1XM_017006202.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.478T=0.522
1000GenomesAmericanSub694C=0.910T=0.090
1000GenomesEast AsianSub1008C=0.989T=0.011
1000GenomesEuropeSub1006C=0.935T=0.065
1000GenomesGlobalStudy-wide5008C=0.815T=0.185
1000GenomesSouth AsianSub978C=0.900T=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.946T=0.054
The Genome Aggregation DatabaseAfricanSub8700C=0.524T=0.476
The Genome Aggregation DatabaseAmericanSub838C=0.940T=0.060
The Genome Aggregation DatabaseEast AsianSub1620C=0.990T=0.010
The Genome Aggregation DatabaseEuropeSub18474C=0.947T=0.052
The Genome Aggregation DatabaseGlobalStudy-wide29934C=0.826T=0.174
The Genome Aggregation DatabaseOtherSub302C=0.930T=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.750T=0.249
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.946T=0.054
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs76391090.000792alcohol dependence21314694

eQTL of rs7639109 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 rs7639109 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 )
chr3143005328143005569E06711134
chr3143006343143006541E06712149
chr3143007784143008171E06713590
chr3143010645143010841E06716451
chr3143010853143010944E06716659
chr3143010975143011211E06716781
chr3143005328143005569E06811134
chr3143006343143006541E06812149
chr3143007784143008171E06813590
chr3143010645143010841E06816451
chr3143010853143010944E06816659
chr3143010975143011211E06816781
chr3143032753143033804E06838559
chr3143034598143034658E06840404
chr3143005328143005569E06911134
chr3143006343143006541E06912149
chr3143007784143008171E06913590
chr3142985862142986190E071-8004
chr3143005328143005569E07111134
chr3143006343143006541E07112149
chr3143007784143008171E07113590
chr3143009279143009333E07115085
chr3143010645143010841E07116451
chr3143010853143010944E07116659
chr3143010975143011211E07116781
chr3143032753143033804E07138559
chr3143034598143034658E07140404
chr3143003002143003052E0728808
chr3143005328143005569E07211134
chr3143007784143008171E07213590
chr3143010645143010841E07216451
chr3143010853143010944E07216659
chr3143021314143021457E07227120
chr3143021458143022149E07227264
chr3143006343143006541E07312149
chr3143010645143010841E07316451
chr3143010853143010944E07316659
chr3142985862142986190E074-8004
chr3143005328143005569E07411134
chr3143006343143006541E07412149
chr3143007784143008171E07413590
chr3143009279143009333E07415085
chr3143010645143010841E07416451
chr3143010853143010944E07416659
chr3143010975143011211E07416781
chr3143011654143011704E07417460
chr3143013051143013262E07418857
chr3143013443143013493E07419249
chr3143014045143014150E07419851
chr3143014155143014380E07419961
chr3143014610143015052E07420416
chr3143015154143015214E07420960
chr3142961011142961247E081-32947
chr3142989803142990292E081-3902
chr3143032753143033804E08138559