rs110420

Homo sapiens
T>C
LMO1 : Intron Variant
LOC105376536 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0412 (12338/29890,GnomAD)
C=0380 (11081/29118,TOPMED)
C=0431 (2158/5008,1000G)
T==0483 (1860/3854,ALSPAC)
T==0494 (1831/3708,TWINSUK)
chr11:8231502 (GRCh38.p7) (11p15.4)
AD
GWASdb2
2   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.8231502T>C
GRCh37.p13 chr 11NC_000011.9:g.8253049T>C
LMO1 RefSeqGeneNG_032827.2:g.42134A>G

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.N/AIntron 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/AGenic Upstream Transcript Variant

Gene: LOC105376536, uncharacterized LOC105376536(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105376536 transcript variant X1XR_001748117.1:n....XR_001748117.1:n.975T>CT>CNon Coding Transcript Variant
LOC105376536 transcript variant X2XR_931013.2:n.N/AIntron Variant
LOC105376536 transcript variant X3XR_931014.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.850C=0.150
1000GenomesAmericanSub694T=0.530C=0.470
1000GenomesEast AsianSub1008T=0.573C=0.427
1000GenomesEuropeSub1006T=0.478C=0.522
1000GenomesGlobalStudy-wide5008T=0.569C=0.431
1000GenomesSouth AsianSub978T=0.310C=0.690
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.483C=0.517
The Genome Aggregation DatabaseAfricanSub8714T=0.796C=0.204
The Genome Aggregation DatabaseAmericanSub830T=0.460C=0.540
The Genome Aggregation DatabaseEast AsianSub1614T=0.549C=0.451
The Genome Aggregation DatabaseEuropeSub18430T=0.498C=0.501
The Genome Aggregation DatabaseGlobalStudy-wide29890T=0.587C=0.412
The Genome Aggregation DatabaseOtherSub302T=0.520C=0.480
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.619C=0.380
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.494C=0.506
PMID Title Author Journal
26030754Candidate Gene Association Analysis of Neuroblastoma in Chinese Children Strengthens the Role of LMO1.Lu JPLoS One
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
rs1104200.000103alcohol consumption23743675

eQTL of rs110420 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 rs110420 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 )
chr1182141658214798E067-38251
chr1182244658224553E067-28496
chr1182246858224772E067-28277
chr1182288918229255E067-23794
chr1182471178247557E067-5492
chr1182475878247752E067-5297
chr1182576448257703E0674595
chr1182783408278429E06725291
chr1182785368278807E06725487
chr1182789138278965E06725864
chr1182789948279044E06725945
chr1182790718279143E06726022
chr1182792648279333E06726215
chr1182795918279693E06726542
chr1182141658214798E068-38251
chr1182174908217598E068-35451
chr1182230828223287E068-29762
chr1182233038224404E068-28645
chr1182292798229446E068-23603
chr1182298698229950E068-23099
chr1182471178247557E068-5492
chr1182475878247752E068-5297
chr1182559918256045E0682942
chr1182560928256441E0683043
chr1182565298256677E0683480
chr1182576448257703E0684595
chr1182783408278429E06825291
chr1182785368278807E06825487
chr1182789138278965E06825864
chr1182789948279044E06825945
chr1182790718279143E06826022
chr1182792648279333E06826215
chr1182795918279693E06826542
chr1182799748280882E06826925
chr1182141658214798E069-38251
chr1182149808215074E069-37975
chr1182230828223287E069-29762
chr1182288918229255E069-23794
chr1182292798229446E069-23603
chr1182303378230425E069-22624
chr1182304768230526E069-22523
chr1182469898247063E069-5986
chr1182471178247557E069-5492
chr1182475878247752E069-5297
chr1182559918256045E0692942
chr1182560928256441E0693043
chr1182565298256677E0693480
chr1182575338257577E0694484
chr1182779198278023E06924870
chr1182783408278429E06925291
chr1182785368278807E06925487
chr1182789138278965E06925864
chr1182789948279044E06925945
chr1182790718279143E06926022
chr1182792648279333E06926215
chr1182795918279693E06926542
chr1182120028212478E070-40571
chr1182129368212986E070-40063
chr1182141658214798E070-38251
chr1182149808215074E070-37975
chr1182151258215175E070-37874
chr1182230828223287E070-29762
chr1182233038224404E070-28645
chr1182244658224553E070-28496
chr1182246858224772E070-28277
chr1182249408225000E070-28049
chr1182252078225257E070-27792
chr1182252998225366E070-27683
chr1182255438225620E070-27429
chr1182256608225977E070-27072
chr1182261598226222E070-26827
chr1182264278226477E070-26572
chr1182267978226871E070-26178
chr1182288918229255E070-23794
chr1182292798229446E070-23603
chr1182430208243070E070-9979
chr1182437668244133E070-8916
chr1182441938244283E070-8766
chr1182443348244935E070-8114
chr1182499468250128E070-2921
chr1182502998250349E070-2700
chr1182504018250481E070-2568
chr1182506918251504E070-1545
chr1182516378252009E070-1040
chr1182532748253502E070225
chr1182536868253940E070637
chr1182540288254265E070979
chr1182633968264849E07010347
chr1182649578265310E07011908
chr1182720008272354E07018951
chr1182725038272582E07019454
chr1182726408272708E07019591
chr1182799748280882E07026925
chr1182808878281098E07027838
chr1182138128213999E071-39050
chr1182140058214077E071-38972
chr1182141658214798E071-38251
chr1182149808215074E071-37975
chr1182151258215175E071-37874
chr1182230828223287E071-29762
chr1182233038224404E071-28645
chr1182244658224553E071-28496
chr1182246858224772E071-28277
chr1182249408225000E071-28049
chr1182252078225257E071-27792
chr1182252998225366E071-27683
chr1182255438225620E071-27429
chr1182256608225977E071-27072
chr1182288918229255E071-23794
chr1182292798229446E071-23603
chr1182471178247557E071-5492
chr1182475878247752E071-5297
chr1182559918256045E0712942
chr1182560928256441E0713043
chr1182565298256677E0713480
chr1182779198278023E07124870
chr1182783408278429E07125291
chr1182789948279044E07125945
chr1182790718279143E07126022
chr1182792648279333E07126215
chr1182795918279693E07126542
chr1182799748280882E07126925
chr1182808878281098E07127838
chr1182815788281656E07128529
chr1182816888281811E07128639
chr1182818868281964E07128837
chr1182140058214077E072-38972
chr1182141658214798E072-38251
chr1182174908217598E072-35451
chr1182233038224404E072-28645
chr1182244658224553E072-28496
chr1182288918229255E072-23794
chr1182292798229446E072-23603
chr1182559918256045E0722942
chr1182560928256441E0723043
chr1182565298256677E0723480
chr1182575338257577E0724484
chr1182783408278429E07225291
chr1182785368278807E07225487
chr1182789138278965E07225864
chr1182789948279044E07225945
chr1182790718279143E07226022
chr1182792648279333E07226215
chr1182795918279693E07226542
chr1182799748280882E07226925
chr1182808878281098E07227838
chr1182230828223287E073-29762
chr1182304768230526E073-22523
chr1182471178247557E073-5492
chr1182475878247752E073-5297
chr1182783408278429E07325291
chr1182785368278807E07325487
chr1182789138278965E07325864
chr1182789948279044E07325945
chr1182790718279143E07326022
chr1182792648279333E07326215
chr1182795918279693E07326542
chr1182140058214077E074-38972
chr1182141658214798E074-38251
chr1182184308218604E074-34445
chr1182188078219043E074-34006
chr1182233038224404E074-28645
chr1182244658224553E074-28496
chr1182288918229255E074-23794
chr1182292798229446E074-23603
chr1182298698229950E074-23099
chr1182559918256045E0742942
chr1182560928256441E0743043
chr1182565298256677E0743480
chr1182575338257577E0744484
chr1182779198278023E07424870
chr1182783408278429E07425291
chr1182785368278807E07425487
chr1182789138278965E07425864
chr1182789948279044E07425945
chr1182790718279143E07426022
chr1182792648279333E07426215
chr1182795918279693E07426542
chr1182799748280882E07426925
chr1182230828223287E081-29762
chr1182233038224404E081-28645
chr1182244658224553E081-28496
chr1182246858224772E081-28277
chr1182249408225000E081-28049
chr1182275488228846E081-24203
chr1182288918229255E081-23794
chr1182292798229446E081-23603
chr1182499468250128E081-2921
chr1182502998250349E081-2700
chr1182504018250481E081-2568
chr1182506918251504E081-1545
chr1182633968264849E08110347
chr1182649578265310E08111908
chr1182720008272354E08118951
chr1182725038272582E08119454
chr1182726408272708E08119591
chr1182731928273250E08120143
chr1182799748280882E08126925
chr1182808878281098E08127838
chr1182873368287492E08134287
chr1182230828223287E082-29762
chr1182233038224404E082-28645
chr1182244658224553E082-28496
chr1182246858224772E082-28277
chr1182249408225000E082-28049
chr1182471178247557E082-5492
chr1182655408265673E08212491
chr1182658018265868E08212752
chr1182815788281656E08228529
chr1182816888281811E08228639










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1182838608286010E06730811
chr1182893818290871E06736332
chr1182838608286010E06830811
chr1182892868289379E06836237
chr1182893818290871E06836332
chr1182838608286010E06930811
chr1182893818290871E06936332
chr1182838608286010E07130811
chr1182893818290871E07136332
chr1182838608286010E07230811
chr1182892868289379E07236237
chr1182838608286010E07330811
chr1182893818290871E07336332
chr1182838608286010E07430811
chr1182893818290871E07436332
chr1182838608286010E08230811
chr1182892868289379E08236237
chr1182893818290871E08236332