rs12574271

Homo sapiens
G>T
LMO1 : Intron Variant
LOC105376536 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0207 (6201/29886,GnomAD)
T=0156 (4560/29118,TOPMED)
T=0127 (634/5008,1000G)
T=0255 (984/3854,ALSPAC)
T=0269 (996/3708,TWINSUK)
chr11:8232956 (GRCh38.p7) (11p15.4)
AD
GWASdb2
1   publication(s)
See rs on genome
212 Enhancers around
18 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.8232956G>T
GRCh37.p13 chr 11NC_000011.9:g.8254503G>T
LMO1 RefSeqGeneNG_032827.2:g.40680C>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.N/AIntron Variant
LMO1 transcript variant X1XM_006718228.3:c.N/AIntron Variant
LMO1 transcript variant X2XM_011520099.2:c.N/AIntron Variant
LMO1 transcript variant X3XM_011520098.2:c.N/AGenic Upstream Transcript 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.1599G>TG>TNon Coding Transcript Variant
LOC105376536 transcript variant X2XR_931013.2:n.705G>TG>TNon Coding Transcript Variant
LOC105376536 transcript variant X3XR_931014.2:n.577G>TG>TNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.964T=0.036
1000GenomesAmericanSub694G=0.920T=0.080
1000GenomesEast AsianSub1008G=0.829T=0.171
1000GenomesEuropeSub1006G=0.739T=0.261
1000GenomesGlobalStudy-wide5008G=0.873T=0.127
1000GenomesSouth AsianSub978G=0.900T=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.745T=0.255
The Genome Aggregation DatabaseAfricanSub8710G=0.928T=0.072
The Genome Aggregation DatabaseAmericanSub834G=0.900T=0.100
The Genome Aggregation DatabaseEast AsianSub1616G=0.847T=0.153
The Genome Aggregation DatabaseEuropeSub18424G=0.719T=0.280
The Genome Aggregation DatabaseGlobalStudy-wide29886G=0.792T=0.207
The Genome Aggregation DatabaseOtherSub302G=0.770T=0.230
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.843T=0.156
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.731T=0.269
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
rs125742711.81E-05alcohol consumption23743675

eQTL of rs12574271 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 rs12574271 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 )
chr1182141658214798E067-39705
chr1182244658224553E067-29950
chr1182246858224772E067-29731
chr1182288918229255E067-25248
chr1182471178247557E067-6946
chr1182475878247752E067-6751
chr1182576448257703E0673141
chr1182783408278429E06723837
chr1182785368278807E06724033
chr1182789138278965E06724410
chr1182789948279044E06724491
chr1182790718279143E06724568
chr1182792648279333E06724761
chr1182795918279693E06725088
chr1182141658214798E068-39705
chr1182174908217598E068-36905
chr1182230828223287E068-31216
chr1182233038224404E068-30099
chr1182292798229446E068-25057
chr1182298698229950E068-24553
chr1182471178247557E068-6946
chr1182475878247752E068-6751
chr1182559918256045E0681488
chr1182560928256441E0681589
chr1182565298256677E0682026
chr1182576448257703E0683141
chr1182783408278429E06823837
chr1182785368278807E06824033
chr1182789138278965E06824410
chr1182789948279044E06824491
chr1182790718279143E06824568
chr1182792648279333E06824761
chr1182795918279693E06825088
chr1182799748280882E06825471
chr1182141658214798E069-39705
chr1182149808215074E069-39429
chr1182230828223287E069-31216
chr1182288918229255E069-25248
chr1182292798229446E069-25057
chr1182303378230425E069-24078
chr1182304768230526E069-23977
chr1182469898247063E069-7440
chr1182471178247557E069-6946
chr1182475878247752E069-6751
chr1182559918256045E0691488
chr1182560928256441E0691589
chr1182565298256677E0692026
chr1182575338257577E0693030
chr1182779198278023E06923416
chr1182783408278429E06923837
chr1182785368278807E06924033
chr1182789138278965E06924410
chr1182789948279044E06924491
chr1182790718279143E06924568
chr1182792648279333E06924761
chr1182795918279693E06925088
chr1182120028212478E070-42025
chr1182129368212986E070-41517
chr1182141658214798E070-39705
chr1182149808215074E070-39429
chr1182151258215175E070-39328
chr1182230828223287E070-31216
chr1182233038224404E070-30099
chr1182244658224553E070-29950
chr1182246858224772E070-29731
chr1182249408225000E070-29503
chr1182252078225257E070-29246
chr1182252998225366E070-29137
chr1182255438225620E070-28883
chr1182256608225977E070-28526
chr1182261598226222E070-28281
chr1182264278226477E070-28026
chr1182267978226871E070-27632
chr1182288918229255E070-25248
chr1182292798229446E070-25057
chr1182430208243070E070-11433
chr1182437668244133E070-10370
chr1182441938244283E070-10220
chr1182443348244935E070-9568
chr1182499468250128E070-4375
chr1182502998250349E070-4154
chr1182504018250481E070-4022
chr1182506918251504E070-2999
chr1182516378252009E070-2494
chr1182532748253502E070-1001
chr1182536868253940E070-563
chr1182540288254265E070-238
chr1182633968264849E0708893
chr1182649578265310E07010454
chr1182720008272354E07017497
chr1182725038272582E07018000
chr1182726408272708E07018137
chr1182799748280882E07025471
chr1182808878281098E07026384
chr1183038308303880E07049327
chr1182138128213999E071-40504
chr1182140058214077E071-40426
chr1182141658214798E071-39705
chr1182149808215074E071-39429
chr1182151258215175E071-39328
chr1182230828223287E071-31216
chr1182233038224404E071-30099
chr1182244658224553E071-29950
chr1182246858224772E071-29731
chr1182249408225000E071-29503
chr1182252078225257E071-29246
chr1182252998225366E071-29137
chr1182255438225620E071-28883
chr1182256608225977E071-28526
chr1182288918229255E071-25248
chr1182292798229446E071-25057
chr1182471178247557E071-6946
chr1182475878247752E071-6751
chr1182559918256045E0711488
chr1182560928256441E0711589
chr1182565298256677E0712026
chr1182779198278023E07123416
chr1182783408278429E07123837
chr1182789948279044E07124491
chr1182790718279143E07124568
chr1182792648279333E07124761
chr1182795918279693E07125088
chr1182799748280882E07125471
chr1182808878281098E07126384
chr1182815788281656E07127075
chr1182816888281811E07127185
chr1182818868281964E07127383
chr1182140058214077E072-40426
chr1182141658214798E072-39705
chr1182174908217598E072-36905
chr1182233038224404E072-30099
chr1182244658224553E072-29950
chr1182288918229255E072-25248
chr1182292798229446E072-25057
chr1182559918256045E0721488
chr1182560928256441E0721589
chr1182565298256677E0722026
chr1182575338257577E0723030
chr1182783408278429E07223837
chr1182785368278807E07224033
chr1182789138278965E07224410
chr1182789948279044E07224491
chr1182790718279143E07224568
chr1182792648279333E07224761
chr1182795918279693E07225088
chr1182799748280882E07225471
chr1182808878281098E07226384
chr1182230828223287E073-31216
chr1182304768230526E073-23977
chr1182471178247557E073-6946
chr1182475878247752E073-6751
chr1182783408278429E07323837
chr1182785368278807E07324033
chr1182789138278965E07324410
chr1182789948279044E07324491
chr1182790718279143E07324568
chr1182792648279333E07324761
chr1182795918279693E07325088
chr1182140058214077E074-40426
chr1182141658214798E074-39705
chr1182184308218604E074-35899
chr1182188078219043E074-35460
chr1182233038224404E074-30099
chr1182244658224553E074-29950
chr1182288918229255E074-25248
chr1182292798229446E074-25057
chr1182298698229950E074-24553
chr1182559918256045E0741488
chr1182560928256441E0741589
chr1182565298256677E0742026
chr1182575338257577E0743030
chr1182779198278023E07423416
chr1182783408278429E07423837
chr1182785368278807E07424033
chr1182789138278965E07424410
chr1182789948279044E07424491
chr1182790718279143E07424568
chr1182792648279333E07424761
chr1182795918279693E07425088
chr1182799748280882E07425471
chr1182230828223287E081-31216
chr1182233038224404E081-30099
chr1182244658224553E081-29950
chr1182246858224772E081-29731
chr1182249408225000E081-29503
chr1182275488228846E081-25657
chr1182288918229255E081-25248
chr1182292798229446E081-25057
chr1182499468250128E081-4375
chr1182502998250349E081-4154
chr1182504018250481E081-4022
chr1182506918251504E081-2999
chr1182633968264849E0818893
chr1182649578265310E08110454
chr1182720008272354E08117497
chr1182725038272582E08118000
chr1182726408272708E08118137
chr1182731928273250E08118689
chr1182799748280882E08125471
chr1182808878281098E08126384
chr1182873368287492E08132833
chr1183038308303880E08149327
chr1182230828223287E082-31216
chr1182233038224404E082-30099
chr1182244658224553E082-29950
chr1182246858224772E082-29731
chr1182249408225000E082-29503
chr1182471178247557E082-6946
chr1182655408265673E08211037
chr1182658018265868E08211298
chr1182815788281656E08227075
chr1182816888281811E08227185










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1182838608286010E06729357
chr1182893818290871E06734878
chr1182838608286010E06829357
chr1182892868289379E06834783
chr1182893818290871E06834878
chr1182838608286010E06929357
chr1182893818290871E06934878
chr1182838608286010E07129357
chr1182893818290871E07134878
chr1182838608286010E07229357
chr1182892868289379E07234783
chr1182838608286010E07329357
chr1182893818290871E07334878
chr1182838608286010E07429357
chr1182893818290871E07434878
chr1182838608286010E08229357
chr1182892868289379E08234783
chr1182893818290871E08234878