rs4758317

Homo sapiens
C>A
LMO1 : Intron Variant
LOC105376536 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0447 (13374/29884,GnomAD)
C==0419 (12205/29118,TOPMED)
C==0431 (2160/5008,1000G)
C==0441 (1698/3854,ALSPAC)
C==0447 (1656/3708,TWINSUK)
chr11:8229264 (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.8229264C>A
GRCh37.p13 chr 11NC_000011.9:g.8250811C>A
LMO1 RefSeqGeneNG_032827.2:g.44372G>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/AIntron Variant

Gene: LOC105376536, uncharacterized LOC105376536(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC105376536 transcript variant X1XR_001748117.1:n.N/AUpstream Transcript Variant
LOC105376536 transcript variant X2XR_931013.2:n.N/AUpstream Transcript Variant
LOC105376536 transcript variant X3XR_931014.2:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.405A=0.595
1000GenomesAmericanSub694C=0.480A=0.520
1000GenomesEast AsianSub1008C=0.577A=0.423
1000GenomesEuropeSub1006C=0.437A=0.563
1000GenomesGlobalStudy-wide5008C=0.431A=0.569
1000GenomesSouth AsianSub978C=0.270A=0.730
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.441A=0.559
The Genome Aggregation DatabaseAfricanSub8700C=0.407A=0.593
The Genome Aggregation DatabaseAmericanSub834C=0.430A=0.570
The Genome Aggregation DatabaseEast AsianSub1616C=0.550A=0.450
The Genome Aggregation DatabaseEuropeSub18432C=0.459A=0.541
The Genome Aggregation DatabaseGlobalStudy-wide29884C=0.447A=0.552
The Genome Aggregation DatabaseOtherSub302C=0.440A=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.419A=0.580
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.447A=0.553
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
rs47583177E-07alcohol consumption23743675

eQTL of rs4758317 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 rs4758317 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 )
chr1182141658214798E067-36013
chr1182244658224553E067-26258
chr1182246858224772E067-26039
chr1182288918229255E067-21556
chr1182471178247557E067-3254
chr1182475878247752E067-3059
chr1182576448257703E0676833
chr1182783408278429E06727529
chr1182785368278807E06727725
chr1182789138278965E06728102
chr1182789948279044E06728183
chr1182790718279143E06728260
chr1182792648279333E06728453
chr1182795918279693E06728780
chr1182141658214798E068-36013
chr1182174908217598E068-33213
chr1182230828223287E068-27524
chr1182233038224404E068-26407
chr1182292798229446E068-21365
chr1182298698229950E068-20861
chr1182471178247557E068-3254
chr1182475878247752E068-3059
chr1182559918256045E0685180
chr1182560928256441E0685281
chr1182565298256677E0685718
chr1182576448257703E0686833
chr1182783408278429E06827529
chr1182785368278807E06827725
chr1182789138278965E06828102
chr1182789948279044E06828183
chr1182790718279143E06828260
chr1182792648279333E06828453
chr1182795918279693E06828780
chr1182799748280882E06829163
chr1182141658214798E069-36013
chr1182149808215074E069-35737
chr1182230828223287E069-27524
chr1182288918229255E069-21556
chr1182292798229446E069-21365
chr1182303378230425E069-20386
chr1182304768230526E069-20285
chr1182469898247063E069-3748
chr1182471178247557E069-3254
chr1182475878247752E069-3059
chr1182559918256045E0695180
chr1182560928256441E0695281
chr1182565298256677E0695718
chr1182575338257577E0696722
chr1182779198278023E06927108
chr1182783408278429E06927529
chr1182785368278807E06927725
chr1182789138278965E06928102
chr1182789948279044E06928183
chr1182790718279143E06928260
chr1182792648279333E06928453
chr1182795918279693E06928780
chr1182120028212478E070-38333
chr1182129368212986E070-37825
chr1182141658214798E070-36013
chr1182149808215074E070-35737
chr1182151258215175E070-35636
chr1182230828223287E070-27524
chr1182233038224404E070-26407
chr1182244658224553E070-26258
chr1182246858224772E070-26039
chr1182249408225000E070-25811
chr1182252078225257E070-25554
chr1182252998225366E070-25445
chr1182255438225620E070-25191
chr1182256608225977E070-24834
chr1182261598226222E070-24589
chr1182264278226477E070-24334
chr1182267978226871E070-23940
chr1182288918229255E070-21556
chr1182292798229446E070-21365
chr1182430208243070E070-7741
chr1182437668244133E070-6678
chr1182441938244283E070-6528
chr1182443348244935E070-5876
chr1182499468250128E070-683
chr1182502998250349E070-462
chr1182504018250481E070-330
chr1182506918251504E0700
chr1182516378252009E070826
chr1182532748253502E0702463
chr1182536868253940E0702875
chr1182540288254265E0703217
chr1182633968264849E07012585
chr1182649578265310E07014146
chr1182720008272354E07021189
chr1182725038272582E07021692
chr1182726408272708E07021829
chr1182799748280882E07029163
chr1182808878281098E07030076
chr1182138128213999E071-36812
chr1182140058214077E071-36734
chr1182141658214798E071-36013
chr1182149808215074E071-35737
chr1182151258215175E071-35636
chr1182230828223287E071-27524
chr1182233038224404E071-26407
chr1182244658224553E071-26258
chr1182246858224772E071-26039
chr1182249408225000E071-25811
chr1182252078225257E071-25554
chr1182252998225366E071-25445
chr1182255438225620E071-25191
chr1182256608225977E071-24834
chr1182288918229255E071-21556
chr1182292798229446E071-21365
chr1182471178247557E071-3254
chr1182475878247752E071-3059
chr1182559918256045E0715180
chr1182560928256441E0715281
chr1182565298256677E0715718
chr1182779198278023E07127108
chr1182783408278429E07127529
chr1182789948279044E07128183
chr1182790718279143E07128260
chr1182792648279333E07128453
chr1182795918279693E07128780
chr1182799748280882E07129163
chr1182808878281098E07130076
chr1182815788281656E07130767
chr1182816888281811E07130877
chr1182818868281964E07131075
chr1182140058214077E072-36734
chr1182141658214798E072-36013
chr1182174908217598E072-33213
chr1182233038224404E072-26407
chr1182244658224553E072-26258
chr1182288918229255E072-21556
chr1182292798229446E072-21365
chr1182559918256045E0725180
chr1182560928256441E0725281
chr1182565298256677E0725718
chr1182575338257577E0726722
chr1182783408278429E07227529
chr1182785368278807E07227725
chr1182789138278965E07228102
chr1182789948279044E07228183
chr1182790718279143E07228260
chr1182792648279333E07228453
chr1182795918279693E07228780
chr1182799748280882E07229163
chr1182808878281098E07230076
chr1182230828223287E073-27524
chr1182304768230526E073-20285
chr1182471178247557E073-3254
chr1182475878247752E073-3059
chr1182783408278429E07327529
chr1182785368278807E07327725
chr1182789138278965E07328102
chr1182789948279044E07328183
chr1182790718279143E07328260
chr1182792648279333E07328453
chr1182795918279693E07328780
chr1182140058214077E074-36734
chr1182141658214798E074-36013
chr1182184308218604E074-32207
chr1182188078219043E074-31768
chr1182233038224404E074-26407
chr1182244658224553E074-26258
chr1182288918229255E074-21556
chr1182292798229446E074-21365
chr1182298698229950E074-20861
chr1182559918256045E0745180
chr1182560928256441E0745281
chr1182565298256677E0745718
chr1182575338257577E0746722
chr1182779198278023E07427108
chr1182783408278429E07427529
chr1182785368278807E07427725
chr1182789138278965E07428102
chr1182789948279044E07428183
chr1182790718279143E07428260
chr1182792648279333E07428453
chr1182795918279693E07428780
chr1182799748280882E07429163
chr1182230828223287E081-27524
chr1182233038224404E081-26407
chr1182244658224553E081-26258
chr1182246858224772E081-26039
chr1182249408225000E081-25811
chr1182275488228846E081-21965
chr1182288918229255E081-21556
chr1182292798229446E081-21365
chr1182499468250128E081-683
chr1182502998250349E081-462
chr1182504018250481E081-330
chr1182506918251504E0810
chr1182633968264849E08112585
chr1182649578265310E08114146
chr1182720008272354E08121189
chr1182725038272582E08121692
chr1182726408272708E08121829
chr1182731928273250E08122381
chr1182799748280882E08129163
chr1182808878281098E08130076
chr1182873368287492E08136525
chr1182230828223287E082-27524
chr1182233038224404E082-26407
chr1182244658224553E082-26258
chr1182246858224772E082-26039
chr1182249408225000E082-25811
chr1182471178247557E082-3254
chr1182655408265673E08214729
chr1182658018265868E08214990
chr1182815788281656E08230767
chr1182816888281811E08230877










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1182838608286010E06733049
chr1182893818290871E06738570
chr1182838608286010E06833049
chr1182892868289379E06838475
chr1182893818290871E06838570
chr1182838608286010E06933049
chr1182893818290871E06938570
chr1182838608286010E07133049
chr1182893818290871E07138570
chr1182838608286010E07233049
chr1182892868289379E07238475
chr1182838608286010E07333049
chr1182893818290871E07338570
chr1182838608286010E07433049
chr1182893818290871E07438570
chr1182838608286010E08233049
chr1182892868289379E08238475
chr1182893818290871E08238570