rs6775025

Homo sapiens
T>C
SLC9A9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0129 (3871/29954,GnomAD)
C=0110 (3218/29118,TOPMED)
C=0113 (566/5008,1000G)
C=0132 (507/3854,ALSPAC)
C=0137 (507/3708,TWINSUK)
chr3:143350462 (GRCh38.p7) (3q24)
ND
GWASdb2
2   publication(s)
See rs on genome
89 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.143350462T>C
GRCh37.p13 chr 3NC_000003.11:g.143069304T>C
SLC9A9 RefSeqGeneNG_017077.1:g.503070A>G

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 X1XM_017006202.1: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

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.936C=0.064
1000GenomesAmericanSub694T=0.930C=0.070
1000GenomesEast AsianSub1008T=0.858C=0.142
1000GenomesEuropeSub1006T=0.881C=0.119
1000GenomesGlobalStudy-wide5008T=0.887C=0.113
1000GenomesSouth AsianSub978T=0.830C=0.170
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.868C=0.132
The Genome Aggregation DatabaseAfricanSub8720T=0.915C=0.085
The Genome Aggregation DatabaseAmericanSub838T=0.920C=0.080
The Genome Aggregation DatabaseEast AsianSub1616T=0.856C=0.144
The Genome Aggregation DatabaseEuropeSub18478T=0.848C=0.151
The Genome Aggregation DatabaseGlobalStudy-wide29954T=0.870C=0.129
The Genome Aggregation DatabaseOtherSub302T=0.910C=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.889C=0.110
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.863C=0.137
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet
25002837An inside job: how endosomal Na(+)/H(+) exchangers link to autism and neurological disease.Kondapalli KCFront Cell Neurosci

P-Value

SNP ID p-value Traits Study
rs67750250.000608nicotine smoking19268276

eQTL of rs6775025 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 rs6775025 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 )
chr3143048485143048606E067-20698
chr3143049956143050074E067-19230
chr3143050233143050516E067-18788
chr3143061820143062271E067-7033
chr3143062591143062850E067-6454
chr3143032753143033804E068-35500
chr3143034598143034658E068-34646
chr3143048485143048606E068-20698
chr3143048684143049027E068-20277
chr3143049079143049314E068-19990
chr3143049352143049544E068-19760
chr3143049735143049860E068-19444
chr3143049956143050074E068-19230
chr3143050233143050516E068-18788
chr3143062591143062850E068-6454
chr3143077113143077227E0687809
chr3143077303143077353E0687999
chr3143077831143077881E0688527
chr3143078088143078343E0688784
chr3143048485143048606E069-20698
chr3143048684143049027E069-20277
chr3143049079143049314E069-19990
chr3143049352143049544E069-19760
chr3143049735143049860E069-19444
chr3143049956143050074E069-19230
chr3143050233143050516E069-18788
chr3143077113143077227E0697809
chr3143077303143077353E0697999
chr3143077831143077881E0698527
chr3143078088143078343E0698784
chr3143032753143033804E071-35500
chr3143034598143034658E071-34646
chr3143049352143049544E071-19760
chr3143049735143049860E071-19444
chr3143049956143050074E071-19230
chr3143050233143050516E071-18788
chr3143050544143051256E071-18048
chr3143062591143062850E071-6454
chr3143077113143077227E0717809
chr3143077303143077353E0717999
chr3143021314143021457E072-47847
chr3143021458143022149E072-47155
chr3143048485143048606E072-20698
chr3143049352143049544E072-19760
chr3143049735143049860E072-19444
chr3143049956143050074E072-19230
chr3143050233143050516E072-18788
chr3143077113143077227E0727809
chr3143077303143077353E0727999
chr3143077831143077881E0728527
chr3143078088143078343E0728784
chr3143048485143048606E073-20698
chr3143048684143049027E073-20277
chr3143049735143049860E073-19444
chr3143049956143050074E073-19230
chr3143049079143049314E074-19990
chr3143049352143049544E074-19760
chr3143049735143049860E074-19444
chr3143049956143050074E074-19230
chr3143050233143050516E074-18788
chr3143062591143062850E074-6454
chr3143062891143063112E074-6192
chr3143063169143063255E074-6049
chr3143063497143063728E074-5576
chr3143077113143077227E0747809
chr3143077303143077353E0747999
chr3143077831143077881E0748527
chr3143078088143078343E0748784
chr3143032753143033804E081-35500
chr3143047831143047907E081-21397
chr3143048485143048606E081-20698
chr3143048684143049027E081-20277
chr3143049079143049314E081-19990
chr3143049352143049544E081-19760
chr3143049735143049860E081-19444
chr3143049956143050074E081-19230
chr3143050233143050516E081-18788
chr3143050544143051256E081-18048
chr3143052386143052488E081-16816
chr3143047365143047584E082-21720
chr3143047831143047907E082-21397
chr3143048485143048606E082-20698
chr3143048684143049027E082-20277
chr3143049079143049314E082-19990
chr3143049352143049544E082-19760
chr3143049735143049860E082-19444
chr3143049956143050074E082-19230
chr3143051973143052092E082-17212
chr3143052386143052488E082-16816