rs4839669

Homo sapiens
G>C
SLC9A9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0427 (12784/29898,GnomAD)
G==0482 (14059/29118,TOPMED)
G==0468 (2346/5008,1000G)
G==0312 (1204/3854,ALSPAC)
G==0310 (1150/3708,TWINSUK)
chr3:143823101 (GRCh38.p7) (3q24)
ND
GWASdb2
2   publication(s)
See rs on genome
172 Enhancers around
26 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.143823101G>C
GRCh37.p13 chr 3NC_000003.11:g.143541943G>C
SLC9A9 RefSeqGeneNG_017077.1:g.30431C>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 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
SLC9A9 transcript variant X3XM_011512703.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.756C=0.244
1000GenomesAmericanSub694G=0.380C=0.620
1000GenomesEast AsianSub1008G=0.382C=0.618
1000GenomesEuropeSub1006G=0.264C=0.736
1000GenomesGlobalStudy-wide5008G=0.468C=0.532
1000GenomesSouth AsianSub978G=0.440C=0.560
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.312C=0.688
The Genome Aggregation DatabaseAfricanSub8692G=0.708C=0.292
The Genome Aggregation DatabaseAmericanSub832G=0.400C=0.600
The Genome Aggregation DatabaseEast AsianSub1608G=0.364C=0.636
The Genome Aggregation DatabaseEuropeSub18464G=0.304C=0.695
The Genome Aggregation DatabaseGlobalStudy-wide29898G=0.427C=0.572
The Genome Aggregation DatabaseOtherSub302G=0.290C=0.710
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.482C=0.517
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.310C=0.690
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
rs48396690.000123nicotine smoking19268276

eQTL of rs4839669 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 rs4839669 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 )
chr3143494209143494320E067-47623
chr3143494346143494566E067-47377
chr3143506169143506266E067-35677
chr3143527871143528678E067-13265
chr3143528815143529371E067-12572
chr3143529436143529492E067-12451
chr3143529518143529592E067-12351
chr3143541726143541861E067-82
chr3143541951143542011E0678
chr3143553028143553194E06711085
chr3143553892143554028E06711949
chr3143554166143554639E06712223
chr3143554683143554822E06712740
chr3143568622143568707E06726679
chr3143568713143569046E06726770
chr3143569094143569267E06727151
chr3143494209143494320E068-47623
chr3143494346143494566E068-47377
chr3143494806143494862E068-47081
chr3143505197143505278E068-36665
chr3143506169143506266E068-35677
chr3143506410143506460E068-35483
chr3143514719143514833E068-27110
chr3143514860143515120E068-26823
chr3143527871143528678E068-13265
chr3143528815143529371E068-12572
chr3143529436143529492E068-12451
chr3143529518143529592E068-12351
chr3143529657143529707E068-12236
chr3143529874143529944E068-11999
chr3143541305143541546E068-397
chr3143541726143541861E068-82
chr3143541951143542011E0688
chr3143550114143550520E0688171
chr3143553892143554028E06811949
chr3143554166143554639E06812223
chr3143554683143554822E06812740
chr3143558095143558182E06816152
chr3143561660143561759E06819717
chr3143563223143563268E06821280
chr3143494209143494320E069-47623
chr3143494346143494566E069-47377
chr3143506169143506266E069-35677
chr3143527871143528678E069-13265
chr3143528815143529371E069-12572
chr3143529436143529492E069-12451
chr3143529518143529592E069-12351
chr3143529657143529707E069-12236
chr3143539800143539925E069-2018
chr3143539969143540019E069-1924
chr3143540052143540130E069-1813
chr3143541305143541546E069-397
chr3143541726143541861E069-82
chr3143541951143542011E0698
chr3143553892143554028E06911949
chr3143554166143554639E06912223
chr3143554683143554822E06912740
chr3143555977143556215E06914034
chr3143556498143556548E06914555
chr3143558928143559082E06916985
chr3143559121143559269E06917178
chr3143559464143559514E06917521
chr3143559620143559701E06917677
chr3143559984143560137E06918041
chr3143564450143564500E06922507
chr3143569484143569555E06927541
chr3143494806143494862E071-47081
chr3143506169143506266E071-35677
chr3143527871143528678E071-13265
chr3143528815143529371E071-12572
chr3143529436143529492E071-12451
chr3143529518143529592E071-12351
chr3143529657143529707E071-12236
chr3143529874143529944E071-11999
chr3143530049143530114E071-11829
chr3143530572143530702E071-11241
chr3143539800143539925E071-2018
chr3143539969143540019E071-1924
chr3143540052143540130E071-1813
chr3143541305143541546E071-397
chr3143541726143541861E071-82
chr3143541951143542011E0718
chr3143553892143554028E07111949
chr3143554166143554639E07112223
chr3143554683143554822E07112740
chr3143555977143556215E07114034
chr3143556498143556548E07114555
chr3143558095143558182E07116152
chr3143563223143563268E07121280
chr3143564450143564500E07122507
chr3143568622143568707E07126679
chr3143568713143569046E07126770
chr3143569094143569267E07127151
chr3143569340143569396E07127397
chr3143569484143569555E07127541
chr3143494209143494320E072-47623
chr3143505197143505278E072-36665
chr3143506169143506266E072-35677
chr3143514410143514460E072-27483
chr3143514719143514833E072-27110
chr3143514860143515120E072-26823
chr3143527871143528678E072-13265
chr3143528815143529371E072-12572
chr3143529436143529492E072-12451
chr3143529518143529592E072-12351
chr3143529657143529707E072-12236
chr3143529874143529944E072-11999
chr3143539800143539925E072-2018
chr3143539969143540019E072-1924
chr3143540052143540130E072-1813
chr3143541305143541546E072-397
chr3143541726143541861E072-82
chr3143553028143553194E07211085
chr3143553892143554028E07211949
chr3143554166143554639E07212223
chr3143558928143559082E07216985
chr3143559121143559269E07217178
chr3143559464143559514E07217521
chr3143559620143559701E07217677
chr3143568713143569046E07226770
chr3143569094143569267E07227151
chr3143569340143569396E07227397
chr3143569484143569555E07227541
chr3143570665143570740E07228722
chr3143514719143514833E073-27110
chr3143528815143529371E073-12572
chr3143541305143541546E073-397
chr3143541726143541861E073-82
chr3143541951143542011E0738
chr3143554683143554822E07312740
chr3143561660143561759E07319717
chr3143505197143505278E074-36665
chr3143506169143506266E074-35677
chr3143514860143515120E074-26823
chr3143526045143526125E074-15818
chr3143528815143529371E074-12572
chr3143529436143529492E074-12451
chr3143529518143529592E074-12351
chr3143529657143529707E074-12236
chr3143529874143529944E074-11999
chr3143530049143530114E074-11829
chr3143530572143530702E074-11241
chr3143539800143539925E074-2018
chr3143539969143540019E074-1924
chr3143540052143540130E074-1813
chr3143541305143541546E074-397
chr3143541726143541861E074-82
chr3143541951143542011E0748
chr3143543322143544142E0741379
chr3143544374143544730E0742431
chr3143550114143550520E0748171
chr3143551350143551578E0749407
chr3143553028143553194E07411085
chr3143553892143554028E07411949
chr3143554166143554639E07412223
chr3143554683143554822E07412740
chr3143555977143556215E07414034
chr3143556498143556548E07414555
chr3143558095143558182E07416152
chr3143558928143559082E07416985
chr3143559121143559269E07417178
chr3143559464143559514E07417521
chr3143559620143559701E07417677
chr3143559984143560137E07418041
chr3143563223143563268E07421280
chr3143564450143564500E07422507
chr3143568622143568707E07426679
chr3143568713143569046E07426770
chr3143569094143569267E07427151
chr3143569340143569396E07427397
chr3143569484143569555E07427541
chr3143527871143528678E081-13265








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3143566116143566244E06724173
chr3143566507143567551E06724564
chr3143567585143567715E06725642
chr3143566116143566244E06824173
chr3143566507143567551E06824564
chr3143567585143567715E06825642
chr3143566116143566244E06924173
chr3143566507143567551E06924564
chr3143567585143567715E06925642
chr3143566116143566244E07024173
chr3143566507143567551E07024564
chr3143566116143566244E07124173
chr3143566507143567551E07124564
chr3143567585143567715E07125642
chr3143566116143566244E07224173
chr3143566507143567551E07224564
chr3143567585143567715E07225642
chr3143566116143566244E07324173
chr3143566507143567551E07324564
chr3143567585143567715E07325642
chr3143566116143566244E07424173
chr3143566507143567551E07424564
chr3143567585143567715E07425642
chr3143566507143567551E08124564
chr3143567585143567715E08125642
chr3143566507143567551E08224564