rs11717973

Homo sapiens
C>T
ITGA9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0469 (14039/29902,GnomAD)
T=0448 (13070/29118,TOPMED)
C==0478 (2396/5008,1000G)
C==0495 (1906/3854,ALSPAC)
C==0492 (1825/3708,TWINSUK)
chr3:37720523 (GRCh38.p7) (3p22.2)
ND
GWASdb2
1   publication(s)
See rs on genome
48 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.37720523C>T
GRCh37.p13 chr 3NC_000003.11:g.37762014C>T
ITGA9 RefSeqGeneNG_016166.1:g.273202C>T

Gene: ITGA9, integrin subunit alpha 9(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ITGA9 transcriptNM_002207.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.617T=0.383
1000GenomesAmericanSub694C=0.490T=0.510
1000GenomesEast AsianSub1008C=0.436T=0.564
1000GenomesEuropeSub1006C=0.516T=0.484
1000GenomesGlobalStudy-wide5008C=0.478T=0.522
1000GenomesSouth AsianSub978C=0.290T=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.495T=0.505
The Genome Aggregation DatabaseAfricanSub8704C=0.585T=0.415
The Genome Aggregation DatabaseAmericanSub834C=0.450T=0.550
The Genome Aggregation DatabaseEast AsianSub1608C=0.467T=0.533
The Genome Aggregation DatabaseEuropeSub18454C=0.513T=0.486
The Genome Aggregation DatabaseGlobalStudy-wide29902C=0.530T=0.469
The Genome Aggregation DatabaseOtherSub302C=0.560T=0.440
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.551T=0.448
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.492T=0.508
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
rs117179730.000476nicotine smoking19268276

eQTL of rs11717973 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 rs11717973 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr33773512437736312E067-25702
chr33773641637736535E067-25479
chr33778323137783432E06721217
chr33773136137731509E068-30505
chr33775449837754615E068-7399
chr33775463337755280E068-6734
chr33780470937805445E06842695
chr33773512437736312E069-25702
chr33773641637736535E069-25479
chr33775400637754289E069-7725
chr33775449837754615E069-7399
chr33775463337755280E069-6734
chr33775528237755369E069-6645
chr33780470937805445E06942695
chr33780549437805619E06943480
chr33774509537745448E070-16566
chr33774552837745690E070-16324
chr33772169937722589E071-39425
chr33773512437736312E071-25702
chr33773641637736535E071-25479
chr33775463337755280E071-6734
chr33775528237755369E071-6645
chr33775547437755527E071-6487
chr33778323137783432E07121217
chr33780470937805445E07142695
chr33780549437805619E07143480
chr33773512437736312E072-25702
chr33773641637736535E072-25479
chr33773674737736942E072-25072
chr33775547437755527E072-6487
chr33780470937805445E07242695
chr33780549437805619E07243480
chr33775449837754615E073-7399
chr33775463337755280E073-6734
chr33775528237755369E073-6645
chr33780470937805445E07342695
chr33780549437805619E07343480
chr33773512437736312E074-25702
chr33773641637736535E074-25479
chr33775449837754615E074-7399
chr33775463337755280E074-6734
chr33775528237755369E074-6645
chr33775547437755527E074-6487
chr33780470937805445E07442695
chr33780549437805619E07443480
chr33773075137730857E081-31157
chr33773512437736312E081-25702
chr33775463337755280E081-6734