rs11041820

Homo sapiens
G>A
LMO1 : Intron Variant
LOC105376536 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0205 (6148/29926,GnomAD)
A=0153 (4475/29118,TOPMED)
A=0128 (643/5008,1000G)
A=0253 (976/3854,ALSPAC)
A=0261 (968/3708,TWINSUK)
chr11:8229891 (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.8229891G>A
GRCh37.p13 chr 11NC_000011.9:g.8251438G>A
LMO1 RefSeqGeneNG_032827.2:g.43745C>T

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.9G>AG>ANon Coding Transcript Variant
LOC105376536 transcript variant X2XR_931013.2:n.9G>AG>ANon Coding Transcript Variant
LOC105376536 transcript variant X3XR_931014.2:n.9G>AG>ANon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.963A=0.037
1000GenomesAmericanSub694G=0.910A=0.090
1000GenomesEast AsianSub1008G=0.821A=0.179
1000GenomesEuropeSub1006G=0.739A=0.261
1000GenomesGlobalStudy-wide5008G=0.872A=0.128
1000GenomesSouth AsianSub978G=0.910A=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.747A=0.253
The Genome Aggregation DatabaseAfricanSub8714G=0.927A=0.073
The Genome Aggregation DatabaseAmericanSub836G=0.900A=0.100
The Genome Aggregation DatabaseEast AsianSub1616G=0.850A=0.150
The Genome Aggregation DatabaseEuropeSub18458G=0.722A=0.277
The Genome Aggregation DatabaseGlobalStudy-wide29926G=0.794A=0.205
The Genome Aggregation DatabaseOtherSub302G=0.780A=0.220
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.846A=0.153
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.739A=0.261
PMID Title Author Journal
26560027Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism.Oldridge DANature
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
rs110418202.31E-05alcohol consumption23743675

eQTL of rs11041820 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 rs11041820 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 )
chr1182141658214798E067-36640
chr1182244658224553E067-26885
chr1182246858224772E067-26666
chr1182288918229255E067-22183
chr1182471178247557E067-3881
chr1182475878247752E067-3686
chr1182576448257703E0676206
chr1182783408278429E06726902
chr1182785368278807E06727098
chr1182789138278965E06727475
chr1182789948279044E06727556
chr1182790718279143E06727633
chr1182792648279333E06727826
chr1182795918279693E06728153
chr1182141658214798E068-36640
chr1182174908217598E068-33840
chr1182230828223287E068-28151
chr1182233038224404E068-27034
chr1182292798229446E068-21992
chr1182298698229950E068-21488
chr1182471178247557E068-3881
chr1182475878247752E068-3686
chr1182559918256045E0684553
chr1182560928256441E0684654
chr1182565298256677E0685091
chr1182576448257703E0686206
chr1182783408278429E06826902
chr1182785368278807E06827098
chr1182789138278965E06827475
chr1182789948279044E06827556
chr1182790718279143E06827633
chr1182792648279333E06827826
chr1182795918279693E06828153
chr1182799748280882E06828536
chr1182141658214798E069-36640
chr1182149808215074E069-36364
chr1182230828223287E069-28151
chr1182288918229255E069-22183
chr1182292798229446E069-21992
chr1182303378230425E069-21013
chr1182304768230526E069-20912
chr1182469898247063E069-4375
chr1182471178247557E069-3881
chr1182475878247752E069-3686
chr1182559918256045E0694553
chr1182560928256441E0694654
chr1182565298256677E0695091
chr1182575338257577E0696095
chr1182779198278023E06926481
chr1182783408278429E06926902
chr1182785368278807E06927098
chr1182789138278965E06927475
chr1182789948279044E06927556
chr1182790718279143E06927633
chr1182792648279333E06927826
chr1182795918279693E06928153
chr1182120028212478E070-38960
chr1182129368212986E070-38452
chr1182141658214798E070-36640
chr1182149808215074E070-36364
chr1182151258215175E070-36263
chr1182230828223287E070-28151
chr1182233038224404E070-27034
chr1182244658224553E070-26885
chr1182246858224772E070-26666
chr1182249408225000E070-26438
chr1182252078225257E070-26181
chr1182252998225366E070-26072
chr1182255438225620E070-25818
chr1182256608225977E070-25461
chr1182261598226222E070-25216
chr1182264278226477E070-24961
chr1182267978226871E070-24567
chr1182288918229255E070-22183
chr1182292798229446E070-21992
chr1182430208243070E070-8368
chr1182437668244133E070-7305
chr1182441938244283E070-7155
chr1182443348244935E070-6503
chr1182499468250128E070-1310
chr1182502998250349E070-1089
chr1182504018250481E070-957
chr1182506918251504E0700
chr1182516378252009E070199
chr1182532748253502E0701836
chr1182536868253940E0702248
chr1182540288254265E0702590
chr1182633968264849E07011958
chr1182649578265310E07013519
chr1182720008272354E07020562
chr1182725038272582E07021065
chr1182726408272708E07021202
chr1182799748280882E07028536
chr1182808878281098E07029449
chr1182138128213999E071-37439
chr1182140058214077E071-37361
chr1182141658214798E071-36640
chr1182149808215074E071-36364
chr1182151258215175E071-36263
chr1182230828223287E071-28151
chr1182233038224404E071-27034
chr1182244658224553E071-26885
chr1182246858224772E071-26666
chr1182249408225000E071-26438
chr1182252078225257E071-26181
chr1182252998225366E071-26072
chr1182255438225620E071-25818
chr1182256608225977E071-25461
chr1182288918229255E071-22183
chr1182292798229446E071-21992
chr1182471178247557E071-3881
chr1182475878247752E071-3686
chr1182559918256045E0714553
chr1182560928256441E0714654
chr1182565298256677E0715091
chr1182779198278023E07126481
chr1182783408278429E07126902
chr1182789948279044E07127556
chr1182790718279143E07127633
chr1182792648279333E07127826
chr1182795918279693E07128153
chr1182799748280882E07128536
chr1182808878281098E07129449
chr1182815788281656E07130140
chr1182816888281811E07130250
chr1182818868281964E07130448
chr1182140058214077E072-37361
chr1182141658214798E072-36640
chr1182174908217598E072-33840
chr1182233038224404E072-27034
chr1182244658224553E072-26885
chr1182288918229255E072-22183
chr1182292798229446E072-21992
chr1182559918256045E0724553
chr1182560928256441E0724654
chr1182565298256677E0725091
chr1182575338257577E0726095
chr1182783408278429E07226902
chr1182785368278807E07227098
chr1182789138278965E07227475
chr1182789948279044E07227556
chr1182790718279143E07227633
chr1182792648279333E07227826
chr1182795918279693E07228153
chr1182799748280882E07228536
chr1182808878281098E07229449
chr1182230828223287E073-28151
chr1182304768230526E073-20912
chr1182471178247557E073-3881
chr1182475878247752E073-3686
chr1182783408278429E07326902
chr1182785368278807E07327098
chr1182789138278965E07327475
chr1182789948279044E07327556
chr1182790718279143E07327633
chr1182792648279333E07327826
chr1182795918279693E07328153
chr1182140058214077E074-37361
chr1182141658214798E074-36640
chr1182184308218604E074-32834
chr1182188078219043E074-32395
chr1182233038224404E074-27034
chr1182244658224553E074-26885
chr1182288918229255E074-22183
chr1182292798229446E074-21992
chr1182298698229950E074-21488
chr1182559918256045E0744553
chr1182560928256441E0744654
chr1182565298256677E0745091
chr1182575338257577E0746095
chr1182779198278023E07426481
chr1182783408278429E07426902
chr1182785368278807E07427098
chr1182789138278965E07427475
chr1182789948279044E07427556
chr1182790718279143E07427633
chr1182792648279333E07427826
chr1182795918279693E07428153
chr1182799748280882E07428536
chr1182230828223287E081-28151
chr1182233038224404E081-27034
chr1182244658224553E081-26885
chr1182246858224772E081-26666
chr1182249408225000E081-26438
chr1182275488228846E081-22592
chr1182288918229255E081-22183
chr1182292798229446E081-21992
chr1182499468250128E081-1310
chr1182502998250349E081-1089
chr1182504018250481E081-957
chr1182506918251504E0810
chr1182633968264849E08111958
chr1182649578265310E08113519
chr1182720008272354E08120562
chr1182725038272582E08121065
chr1182726408272708E08121202
chr1182731928273250E08121754
chr1182799748280882E08128536
chr1182808878281098E08129449
chr1182873368287492E08135898
chr1182230828223287E082-28151
chr1182233038224404E082-27034
chr1182244658224553E082-26885
chr1182246858224772E082-26666
chr1182249408225000E082-26438
chr1182471178247557E082-3881
chr1182655408265673E08214102
chr1182658018265868E08214363
chr1182815788281656E08230140
chr1182816888281811E08230250










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1182838608286010E06732422
chr1182893818290871E06737943
chr1182838608286010E06832422
chr1182892868289379E06837848
chr1182893818290871E06837943
chr1182838608286010E06932422
chr1182893818290871E06937943
chr1182838608286010E07132422
chr1182893818290871E07137943
chr1182838608286010E07232422
chr1182892868289379E07237848
chr1182838608286010E07332422
chr1182893818290871E07337943
chr1182838608286010E07432422
chr1182893818290871E07437943
chr1182838608286010E08232422
chr1182892868289379E08237848
chr1182893818290871E08237943