rs2290450

Homo sapiens
C>T
LMO1 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0205 (20195/98376,ExAC)
T=0201 (6044/29954,GnomAD)
T=0147 (4304/29118,TOPMED)
C==0188 (2368/12576,GO-ESP)
T=0127 (634/5008,1000G)
T=0241 (927/3854,ALSPAC)
T=0253 (937/3708,TWINSUK)
chr11:8226935 (GRCh38.p7) (11p15.4)
AD
GWASdb2
1   publication(s)
See rs on genome
210 Enhancers around
18 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.8226935C>T
GRCh37.p13 chr 11NC_000011.9:g.8248482C>T
LMO1 RefSeqGeneNG_032827.2:g.46701G>A

Gene: LMO1, LIM domain only 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LMO1 transcript variant 2NM_001270428.1:c.N/AIntron Variant
LMO1 transcript variant 1NM_002315.2:c.N/AIntron Variant
LMO1 transcript variant 3NR_073006.1:n.921G>AG>ANon Coding Transcript Variant
LMO1 transcript variant X1XM_006718228.3:c.N/AIntron Variant
LMO1 transcript variant X3XM_011520098.2:c.N/AIntron Variant
LMO1 transcript variant X2XM_011520099.2:c.N/AIntron Variant
LMO1 transcript variant X4XM_011520100.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.963T=0.037
1000GenomesAmericanSub694C=0.920T=0.080
1000GenomesEast AsianSub1008C=0.822T=0.178
1000GenomesEuropeSub1006C=0.744T=0.256
1000GenomesGlobalStudy-wide5008C=0.873T=0.127
1000GenomesSouth AsianSub978C=0.900T=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.759T=0.241
The Exome Aggregation ConsortiumAmericanSub16804C=0.923T=0.076
The Exome Aggregation ConsortiumAsianSub20008C=0.860T=0.139
The Exome Aggregation ConsortiumEuropeSub60876C=0.737T=0.262
The Exome Aggregation ConsortiumGlobalStudy-wide98376C=0.794T=0.205
The Exome Aggregation ConsortiumOtherSub688C=0.790T=0.210
The Genome Aggregation DatabaseAfricanSub8728C=0.930T=0.070
The Genome Aggregation DatabaseAmericanSub834C=0.900T=0.100
The Genome Aggregation DatabaseEast AsianSub1620C=0.840T=0.160
The Genome Aggregation DatabaseEuropeSub18470C=0.727T=0.272
The Genome Aggregation DatabaseGlobalStudy-wide29954C=0.798T=0.201
The Genome Aggregation DatabaseOtherSub302C=0.780T=0.220
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.852T=0.147
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.747T=0.253
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs22904502.52E-05alcohol consumption23743675

eQTL of rs2290450 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 rs2290450 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 )
chr1182141658214798E067-33684
chr1182244658224553E067-23929
chr1182246858224772E067-23710
chr1182288918229255E067-19227
chr1182471178247557E067-925
chr1182475878247752E067-730
chr1182576448257703E0679162
chr1182783408278429E06729858
chr1182785368278807E06730054
chr1182789138278965E06730431
chr1182789948279044E06730512
chr1182790718279143E06730589
chr1182792648279333E06730782
chr1182795918279693E06731109
chr1182141658214798E068-33684
chr1182174908217598E068-30884
chr1182230828223287E068-25195
chr1182233038224404E068-24078
chr1182292798229446E068-19036
chr1182298698229950E068-18532
chr1182471178247557E068-925
chr1182475878247752E068-730
chr1182559918256045E0687509
chr1182560928256441E0687610
chr1182565298256677E0688047
chr1182576448257703E0689162
chr1182783408278429E06829858
chr1182785368278807E06830054
chr1182789138278965E06830431
chr1182789948279044E06830512
chr1182790718279143E06830589
chr1182792648279333E06830782
chr1182795918279693E06831109
chr1182799748280882E06831492
chr1182141658214798E069-33684
chr1182149808215074E069-33408
chr1182230828223287E069-25195
chr1182288918229255E069-19227
chr1182292798229446E069-19036
chr1182303378230425E069-18057
chr1182304768230526E069-17956
chr1182469898247063E069-1419
chr1182471178247557E069-925
chr1182475878247752E069-730
chr1182559918256045E0697509
chr1182560928256441E0697610
chr1182565298256677E0698047
chr1182575338257577E0699051
chr1182779198278023E06929437
chr1182783408278429E06929858
chr1182785368278807E06930054
chr1182789138278965E06930431
chr1182789948279044E06930512
chr1182790718279143E06930589
chr1182792648279333E06930782
chr1182795918279693E06931109
chr1182120028212478E070-36004
chr1182129368212986E070-35496
chr1182141658214798E070-33684
chr1182149808215074E070-33408
chr1182151258215175E070-33307
chr1182230828223287E070-25195
chr1182233038224404E070-24078
chr1182244658224553E070-23929
chr1182246858224772E070-23710
chr1182249408225000E070-23482
chr1182252078225257E070-23225
chr1182252998225366E070-23116
chr1182255438225620E070-22862
chr1182256608225977E070-22505
chr1182261598226222E070-22260
chr1182264278226477E070-22005
chr1182267978226871E070-21611
chr1182288918229255E070-19227
chr1182292798229446E070-19036
chr1182430208243070E070-5412
chr1182437668244133E070-4349
chr1182441938244283E070-4199
chr1182443348244935E070-3547
chr1182499468250128E0701464
chr1182502998250349E0701817
chr1182504018250481E0701919
chr1182506918251504E0702209
chr1182516378252009E0703155
chr1182532748253502E0704792
chr1182536868253940E0705204
chr1182540288254265E0705546
chr1182633968264849E07014914
chr1182649578265310E07016475
chr1182720008272354E07023518
chr1182725038272582E07024021
chr1182726408272708E07024158
chr1182799748280882E07031492
chr1182808878281098E07032405
chr1182138128213999E071-34483
chr1182140058214077E071-34405
chr1182141658214798E071-33684
chr1182149808215074E071-33408
chr1182151258215175E071-33307
chr1182230828223287E071-25195
chr1182233038224404E071-24078
chr1182244658224553E071-23929
chr1182246858224772E071-23710
chr1182249408225000E071-23482
chr1182252078225257E071-23225
chr1182252998225366E071-23116
chr1182255438225620E071-22862
chr1182256608225977E071-22505
chr1182288918229255E071-19227
chr1182292798229446E071-19036
chr1182471178247557E071-925
chr1182475878247752E071-730
chr1182559918256045E0717509
chr1182560928256441E0717610
chr1182565298256677E0718047
chr1182779198278023E07129437
chr1182783408278429E07129858
chr1182789948279044E07130512
chr1182790718279143E07130589
chr1182792648279333E07130782
chr1182795918279693E07131109
chr1182799748280882E07131492
chr1182808878281098E07132405
chr1182815788281656E07133096
chr1182816888281811E07133206
chr1182818868281964E07133404
chr1182140058214077E072-34405
chr1182141658214798E072-33684
chr1182174908217598E072-30884
chr1182233038224404E072-24078
chr1182244658224553E072-23929
chr1182288918229255E072-19227
chr1182292798229446E072-19036
chr1182559918256045E0727509
chr1182560928256441E0727610
chr1182565298256677E0728047
chr1182575338257577E0729051
chr1182783408278429E07229858
chr1182785368278807E07230054
chr1182789138278965E07230431
chr1182789948279044E07230512
chr1182790718279143E07230589
chr1182792648279333E07230782
chr1182795918279693E07231109
chr1182799748280882E07231492
chr1182808878281098E07232405
chr1182230828223287E073-25195
chr1182304768230526E073-17956
chr1182471178247557E073-925
chr1182475878247752E073-730
chr1182783408278429E07329858
chr1182785368278807E07330054
chr1182789138278965E07330431
chr1182789948279044E07330512
chr1182790718279143E07330589
chr1182792648279333E07330782
chr1182795918279693E07331109
chr1182140058214077E074-34405
chr1182141658214798E074-33684
chr1182184308218604E074-29878
chr1182188078219043E074-29439
chr1182233038224404E074-24078
chr1182244658224553E074-23929
chr1182288918229255E074-19227
chr1182292798229446E074-19036
chr1182298698229950E074-18532
chr1182559918256045E0747509
chr1182560928256441E0747610
chr1182565298256677E0748047
chr1182575338257577E0749051
chr1182779198278023E07429437
chr1182783408278429E07429858
chr1182785368278807E07430054
chr1182789138278965E07430431
chr1182789948279044E07430512
chr1182790718279143E07430589
chr1182792648279333E07430782
chr1182795918279693E07431109
chr1182799748280882E07431492
chr1182230828223287E081-25195
chr1182233038224404E081-24078
chr1182244658224553E081-23929
chr1182246858224772E081-23710
chr1182249408225000E081-23482
chr1182275488228846E081-19636
chr1182288918229255E081-19227
chr1182292798229446E081-19036
chr1182499468250128E0811464
chr1182502998250349E0811817
chr1182504018250481E0811919
chr1182506918251504E0812209
chr1182633968264849E08114914
chr1182649578265310E08116475
chr1182720008272354E08123518
chr1182725038272582E08124021
chr1182726408272708E08124158
chr1182731928273250E08124710
chr1182799748280882E08131492
chr1182808878281098E08132405
chr1182873368287492E08138854
chr1182230828223287E082-25195
chr1182233038224404E082-24078
chr1182244658224553E082-23929
chr1182246858224772E082-23710
chr1182249408225000E082-23482
chr1182471178247557E082-925
chr1182655408265673E08217058
chr1182658018265868E08217319
chr1182815788281656E08233096
chr1182816888281811E08233206










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1182838608286010E06735378
chr1182893818290871E06740899
chr1182838608286010E06835378
chr1182892868289379E06840804
chr1182893818290871E06840899
chr1182838608286010E06935378
chr1182893818290871E06940899
chr1182838608286010E07135378
chr1182893818290871E07140899
chr1182838608286010E07235378
chr1182892868289379E07240804
chr1182838608286010E07335378
chr1182893818290871E07340899
chr1182838608286010E07435378
chr1182893818290871E07440899
chr1182838608286010E08235378
chr1182892868289379E08240804
chr1182893818290871E08240899