rs2290451

Homo sapiens
C>A / C>G
LMO1 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0217 (6517/29932,GnomAD)
G=0170 (4966/29118,TOPMED)
G=0142 (709/5008,1000G)
G=0257 (991/3854,ALSPAC)
G=0271 (1004/3708,TWINSUK)
chr11:8226893 (GRCh38.p7) (11p15.4)
AD
GWASdb2
2   publication(s)
See rs on genome
114 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.8226893C>A
GRCh38.p7 chr 11NC_000011.10:g.8226893C>G
GRCh37.p13 chr 11NC_000011.9:g.8248440C>A
GRCh37.p13 chr 11NC_000011.9:g.8248440C>G
LMO1 RefSeqGeneNG_032827.2:g.46743G>T
LMO1 RefSeqGeneNG_032827.2:g.46743G>C

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.963G>TG>TNon Coding Transcript Variant
LMO1 transcript variant 3NR_073006.1:n.963G>CG>CNon 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=0.923G=0.077
1000GenomesAmericanSub694C=0.920G=0.080
1000GenomesEast AsianSub1008C=0.814G=0.186
1000GenomesEuropeSub1006C=0.736G=0.264
1000GenomesGlobalStudy-wide5008C=0.858G=0.142
1000GenomesSouth AsianSub978C=0.900G=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.743G=0.257
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.829G=0.170
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.729G=0.271
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
rs22904512.22E-05alcohol consumption23743675

eQTL of rs2290451 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 rs2290451 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 )
chr118312068883120789E067-36330
chr118312082283120890E067-36229
chr118312099583121312E067-35807
chr118312150583121577E067-35542
chr118312159483121648E067-35471
chr118312191383122589E067-34530
chr118314910983149217E067-7902
chr118318417783184274E06727058
chr118318694583187118E06729826
chr118318732783187505E06730208
chr118319141183191577E06734292
chr118319182483191874E06734705
chr118319195783192060E06734838
chr118312068883120789E068-36330
chr118312082283120890E068-36229
chr118312099583121312E068-35807
chr118312150583121577E068-35542
chr118312159483121648E068-35471
chr118314910983149217E068-7902
chr118314943783149487E068-7632
chr118314950883149659E068-7460
chr118316628983166369E0689170
chr118316639883166686E0689279
chr118316694183167016E0689822
chr118318295583183639E06825836
chr118318694583187118E06829826
chr118318732783187505E06830208
chr118319141183191577E06834292
chr118319182483191874E06834705
chr118319195783192060E06834838
chr118319780283197852E06840683
chr118320081483200864E06843695
chr118320090683200967E06843787
chr118312043383120532E069-36587
chr118312068883120789E069-36330
chr118316694183167016E0699822
chr118316721783167439E06910098
chr118317047783170527E06913358
chr118318280383182885E06925684
chr118318295583183639E06925836
chr118318694583187118E06929826
chr118318732783187505E06930208
chr118319141183191577E06934292
chr118319182483191874E06934705
chr118319195783192060E06934838
chr118319696183197011E06939842
chr118319780283197852E06940683
chr118316694183167016E0709822
chr118316721783167439E07010098
chr118317897983179159E07021860
chr118310901283109052E071-48067
chr118312043383120532E071-36587
chr118312068883120789E071-36330
chr118312082283120890E071-36229
chr118312099583121312E071-35807
chr118312150583121577E071-35542
chr118312159483121648E071-35471
chr118312191383122589E071-34530
chr118314910983149217E071-7902
chr118314943783149487E071-7632
chr118314950883149659E071-7460
chr118316628983166369E0719170
chr118316639883166686E0719279
chr118316694183167016E0719822
chr118318261383182663E07125494
chr118318280383182885E07125684
chr118318295583183639E07125836
chr118319780283197852E07140683
chr118319938383199479E07142264
chr118319976283199812E07142643
chr118320006883200118E07142949
chr118312068883120789E072-36330
chr118312082283120890E072-36229
chr118312099583121312E072-35807
chr118312150583121577E072-35542
chr118312159483121648E072-35471
chr118314910983149217E072-7902
chr118316628983166369E0729170
chr118316639883166686E0729279
chr118316694183167016E0729822
chr118316721783167439E07210098
chr118316811183168189E07210992
chr118317098283171092E07213863
chr118317120383171274E07214084
chr118318280383182885E07225684
chr118319195783192060E07234838
chr118312043383120532E073-36587
chr118312068883120789E073-36330
chr118312082283120890E073-36229
chr118312099583121312E073-35807
chr118316721783167439E07310098
chr118318694583187118E07329826
chr118318732783187505E07330208
chr118311978983120289E074-36830
chr118312043383120532E074-36587
chr118312068883120789E074-36330
chr118312082283120890E074-36229
chr118312099583121312E074-35807
chr118312150583121577E074-35542
chr118312159483121648E074-35471
chr118314910983149217E074-7902
chr118314943783149487E074-7632
chr118314950883149659E074-7460
chr118318694583187118E07429826
chr118319629583196623E07439176
chr118319696183197011E07439842
chr118319938383199479E07442264
chr118314910983149217E081-7902
chr118314943783149487E081-7632
chr118314950883149659E081-7460
chr118314969083149787E081-7332
chr118316694183167016E0819822
chr118316721783167439E08110098
chr118316694183167016E0829822