rs9916609

Homo sapiens
C>A
ITGAE : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0342 (10208/29832,GnomAD)
C==0327 (9545/29118,TOPMED)
C==0466 (2335/5008,1000G)
C==0287 (1105/3854,ALSPAC)
C==0291 (1079/3708,TWINSUK)
chr17:3769220 (GRCh38.p7) (17p13.2)
ND
GWASdb2
1   publication(s)
See rs on genome
79 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.3769220C>A
GRCh37.p13 chr 17NC_000017.10:g.3672514C>A

Gene: ITGAE, integrin subunit alpha E(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ITGAE transcriptNM_002208.4:c.N/AIntron Variant
ITGAE transcript variant X1XM_011523823.2:c.N/AIntron Variant
ITGAE transcript variant X3XM_011523825.2:c.N/AIntron Variant
ITGAE transcript variant X4XM_011523827.2:c.N/AIntron Variant
ITGAE transcript variant X5XM_011523828.2:c.N/AIntron Variant
ITGAE transcript variant X2XM_017024586.1:c.N/AIntron Variant
ITGAE transcript variant X6XM_017024587.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.272A=0.728
1000GenomesAmericanSub694C=0.470A=0.530
1000GenomesEast AsianSub1008C=0.827A=0.173
1000GenomesEuropeSub1006C=0.251A=0.749
1000GenomesGlobalStudy-wide5008C=0.466A=0.534
1000GenomesSouth AsianSub978C=0.570A=0.430
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.287A=0.713
The Genome Aggregation DatabaseAfricanSub8676C=0.293A=0.707
The Genome Aggregation DatabaseAmericanSub838C=0.460A=0.540
The Genome Aggregation DatabaseEast AsianSub1618C=0.821A=0.179
The Genome Aggregation DatabaseEuropeSub18398C=0.316A=0.683
The Genome Aggregation DatabaseGlobalStudy-wide29832C=0.342A=0.657
The Genome Aggregation DatabaseOtherSub302C=0.390A=0.610
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.327A=0.672
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.291A=0.709
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs99166096.03E-05nicotine dependence (smoking)22377092

eQTL of rs9916609 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 rs9916609 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 )
chr1736406713641617E067-30897
chr1736416563641715E067-30799
chr1736417263642521E067-29993
chr1736425423642658E067-29856
chr1736949033695151E06722389
chr1736952643695348E06722750
chr1736958863695995E06723372
chr1736960313696301E06723517
chr1737221703722464E06749656
chr1736233503623888E068-48626
chr1736425423642658E068-29856
chr1736427483643680E068-28834
chr1736940763694189E06821562
chr1736952643695348E06822750
chr1736958863695995E06823372
chr1736960313696301E06823517
chr1736967183696773E06824204
chr1737221703722464E06849656
chr1736376353638236E069-34278
chr1736406713641617E069-30897
chr1736416563641715E069-30799
chr1736417263642521E069-29993
chr1736425423642658E069-29856
chr1736427483643680E069-28834
chr1736949033695151E06922389
chr1736952643695348E06922750
chr1736958863695995E06923372
chr1736960313696301E06923517
chr1736967183696773E06924204
chr1737221703722464E06949656
chr1736417263642521E070-29993
chr1736425423642658E070-29856
chr1736425423642658E071-29856
chr1736427483643680E071-28834
chr1736949033695151E07122389
chr1736952643695348E07122750
chr1736958863695995E07123372
chr1736960313696301E07123517
chr1736969453696985E07124431
chr1737221703722464E07149656
chr1736425423642658E072-29856
chr1736427483643680E072-28834
chr1736589223659476E072-13038
chr1736949033695151E07222389
chr1736952643695348E07222750
chr1736958863695995E07223372
chr1736960313696301E07223517
chr1736967183696773E07224204
chr1736969453696985E07224431
chr1737221703722464E07249656
chr1736417263642521E073-29993
chr1736425423642658E073-29856
chr1736949033695151E07322389
chr1736992893699415E07326775
chr1737221703722464E07349656
chr1736376353638236E074-34278
chr1736406713641617E074-30897
chr1736416563641715E074-30799
chr1736417263642521E074-29993
chr1736425423642658E074-29856
chr1736744173674932E0741903
chr1736751043675160E0742590
chr1736752333675698E0742719
chr1736958863695995E07423372
chr1736960313696301E07423517
chr1737198353719978E07447321
chr1737221703722464E07449656
chr1736576183658917E081-13597
chr1736737373674168E0811223
chr1736744173674932E0811903
chr1736751043675160E0812590
chr1736752333675698E0812719
chr1736958863695995E08123372
chr1736960313696301E08123517
chr1736967183696773E08124204
chr1736949033695151E08222389
chr1736952643695348E08222750
chr1736958863695995E08223372
chr1736960313696301E08223517










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1736261023628263E067-44251
chr1736261023628263E068-44251
chr1736261023628263E069-44251
chr1736261023628263E070-44251
chr1736261023628263E071-44251
chr1736261023628263E072-44251
chr1736261023628263E073-44251
chr1736261023628263E074-44251
chr1736261023628263E082-44251