rs6550481

Homo sapiens
T>A / T>G
ITGA9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0406 (12128/29860,GnomAD)
T==0452 (2263/5008,1000G)
T==0385 (1482/3854,ALSPAC)
T==0375 (1390/3708,TWINSUK)
chr3:37573219 (GRCh38.p7) (3p22.2)
ND
GWASdb2
1   publication(s)
See rs on genome
87 Enhancers around
68 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.37573219T>A
GRCh38.p7 chr 3NC_000003.12:g.37573219T>G
GRCh37.p13 chr 3NC_000003.11:g.37614710T>A
GRCh37.p13 chr 3NC_000003.11:g.37614710T>G
RNU7-73P pseudogeneNG_007689.3:g.95A>T
RNU7-73P pseudogeneNG_007689.3:g.95A>C
ITGA9 RefSeqGeneNG_016166.1:g.125898T>A
ITGA9 RefSeqGeneNG_016166.1:g.125898T>G

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
1000GenomesAfricanSub1322T=0.523G=0.477
1000GenomesAmericanSub694T=0.410G=0.590
1000GenomesEast AsianSub1008T=0.242G=0.758
1000GenomesEuropeSub1006T=0.372G=0.628
1000GenomesGlobalStudy-wide5008T=0.452G=0.548
1000GenomesSouth AsianSub978T=0.690G=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.385G=0.615
The Genome Aggregation DatabaseAfricanSub8676T=0.500G=0.500
The Genome Aggregation DatabaseAmericanSub834T=0.400G=0.600
The Genome Aggregation DatabaseEast AsianSub1618T=0.266G=0.734
The Genome Aggregation DatabaseEuropeSub18430T=0.374G=0.625
The Genome Aggregation DatabaseGlobalStudy-wide29860T=0.406G=0.593
The Genome Aggregation DatabaseOtherSub302T=0.410G=0.590
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.375G=0.625
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
rs65504810.000268nicotine smoking19268276

eQTL of rs6550481 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 rs6550481 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 )
chr35856820658568280E067-21506
chr35860299858603549E06713212
chr35860361458603680E06713828
chr35861427158615450E06724485
chr35861551758616240E06725731
chr35855433758554985E068-34801
chr35856360958563663E068-26123
chr35856367858563731E068-26055
chr35856667058567845E068-21941
chr35856792658567992E068-21794
chr35856820658568280E068-21506
chr35858989558589949E068109
chr35859003658590086E068250
chr35859039458590434E068608
chr35861317258613769E06823386
chr35861379958614145E06824013
chr35861427158615450E06824485
chr35861551758616240E06825731
chr35855433758554985E069-34801
chr35856667058567845E069-21941
chr35856792658567992E069-21794
chr35856820658568280E069-21506
chr35859003658590086E069250
chr35859039458590434E069608
chr35861317258613769E06923386
chr35861379958614145E06924013
chr35861427158615450E06924485
chr35861551758616240E06925731
chr35855663358556693E070-33093
chr35855947458559650E070-30136
chr35855970058559878E070-29908
chr35856667058567845E070-21941
chr35856792658567992E070-21794
chr35856820658568280E070-21506
chr35859448058594695E0704694
chr35861285758612984E07023071
chr35861298758613103E07023201
chr35861317258613769E07023386
chr35861379958614145E07024013
chr35861427158615450E07024485
chr35862637658626754E07036590
chr35856667058567845E071-21941
chr35856792658567992E071-21794
chr35856820658568280E071-21506
chr35861317258613769E07123386
chr35861379958614145E07124013
chr35861427158615450E07124485
chr35861551758616240E07125731
chr35862637658626754E07136590
chr35854122758541298E072-48488
chr35856820658568280E072-21506
chr35860361458603680E07213828
chr35861427158615450E07224485
chr35861551758616240E07225731
chr35862637658626754E07236590
chr35855433758554985E073-34801
chr35855663358556693E073-33093
chr35860719058607663E07317404
chr35861317258613769E07323386
chr35861379958614145E07324013
chr35861427158615450E07324485
chr35861551758616240E07325731
chr35855663358556693E074-33093
chr35856820658568280E074-21506
chr35861285758612984E07423071
chr35861298758613103E07423201
chr35861317258613769E07423386
chr35861379958614145E07424013
chr35861427158615450E07424485
chr35861551758616240E07425731
chr35854241458543562E081-46224
chr35856360958563663E081-26123
chr35856367858563731E081-26055
chr35856667058567845E081-21941
chr35856792658567992E081-21794
chr35861100058611169E08121214
chr35861285758612984E08123071
chr35861298758613103E08123201
chr35863236358632579E08142577
chr35856667058567845E082-21941
chr35856792658567992E082-21794
chr35856820658568280E082-21506
chr35861285758612984E08223071
chr35861298758613103E08223201
chr35861379958614145E08224013
chr35861427158615450E08224485
chr35861551758616240E08225731










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr35856177358561946E067-27840
chr35856200458562242E067-27544
chr35856238158562441E067-27345
chr35856244758562532E067-27254
chr35856260258562682E067-27104
chr35857034658570485E067-19301
chr35857054958571554E067-18232
chr35856177358561946E068-27840
chr35856200458562242E068-27544
chr35856238158562441E068-27345
chr35856244758562532E068-27254
chr35856260258562682E068-27104
chr35857034658570485E068-19301
chr35857054958571554E068-18232
chr35856177358561946E069-27840
chr35856200458562242E069-27544
chr35856238158562441E069-27345
chr35856244758562532E069-27254
chr35856260258562682E069-27104
chr35857034658570485E069-19301
chr35857054958571554E069-18232
chr35856177358561946E070-27840
chr35856200458562242E070-27544
chr35856238158562441E070-27345
chr35856244758562532E070-27254
chr35856260258562682E070-27104
chr35857034658570485E070-19301
chr35857054958571554E070-18232
chr35856177358561946E071-27840
chr35856200458562242E071-27544
chr35856238158562441E071-27345
chr35856244758562532E071-27254
chr35856260258562682E071-27104
chr35857034658570485E071-19301
chr35857054958571554E071-18232
chr35856177358561946E072-27840
chr35856200458562242E072-27544
chr35856238158562441E072-27345
chr35856244758562532E072-27254
chr35856260258562682E072-27104
chr35857034658570485E072-19301
chr35857054958571554E072-18232
chr35856177358561946E073-27840
chr35856200458562242E073-27544
chr35856238158562441E073-27345
chr35856244758562532E073-27254
chr35856260258562682E073-27104
chr35857034658570485E073-19301
chr35857054958571554E073-18232
chr35856177358561946E074-27840
chr35856200458562242E074-27544
chr35856238158562441E074-27345
chr35856244758562532E074-27254
chr35856260258562682E074-27104
chr35857034658570485E074-19301
chr35857054958571554E074-18232
chr35856200458562242E081-27544
chr35856238158562441E081-27345
chr35856244758562532E081-27254
chr35856260258562682E081-27104
chr35857054958571554E081-18232
chr35856177358561946E082-27840
chr35856200458562242E082-27544
chr35856238158562441E082-27345
chr35856244758562532E082-27254
chr35856260258562682E082-27104
chr35857034658570485E082-19301
chr35857054958571554E082-18232