rs2436728

Homo sapiens
G>A
LRFN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0392 (11602/29594,GnomAD)
A=0343 (1717/5008,1000G)
A=0406 (1563/3854,ALSPAC)
A=0413 (1532/3708,TWINSUK)
chr6:40397862 (GRCh38.p7) (6p21.2)
AD
GWASdb2
1   publication(s)
See rs on genome
120 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.40397862G>A
GRCh37.p13 chr 6NC_000006.11:g.40365601G>A

Gene: LRFN2, leucine rich repeat and fibronectin type III domain containing 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LRFN2 transcriptNM_020737.2:c.N/AIntron Variant
LRFN2 transcript variant X1XM_011514761.2:c.N/AIntron Variant
LRFN2 transcript variant X3XM_011514762.2:c.N/AIntron Variant
LRFN2 transcript variant X2XM_017011110.1:c.N/AIntron Variant
LRFN2 transcript variant X4XM_017011111.1:c.N/AGenic Downstream Transcript Variant
LRFN2 transcript variant X7XR_001743534.1:n.N/AGenic Downstream Transcript Variant
LRFN2 transcript variant X8XR_001743535.1:n.N/AGenic Downstream Transcript Variant
LRFN2 transcript variant X5XR_926281.2:n.N/AGenic Downstream Transcript Variant
LRFN2 transcript variant X6XR_926282.2:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.820A=0.180
1000GenomesAmericanSub694G=0.640A=0.360
1000GenomesEast AsianSub1008G=0.445A=0.555
1000GenomesEuropeSub1006G=0.594A=0.406
1000GenomesGlobalStudy-wide5008G=0.657A=0.343
1000GenomesSouth AsianSub978G=0.730A=0.270
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.594A=0.406
The Genome Aggregation DatabaseAfricanSub8644G=0.774A=0.226
The Genome Aggregation DatabaseAmericanSub828G=0.630A=0.370
The Genome Aggregation DatabaseEast AsianSub1612G=0.485A=0.515
The Genome Aggregation DatabaseEuropeSub18210G=0.537A=0.462
The Genome Aggregation DatabaseGlobalStudy-wide29594G=0.608A=0.392
The Genome Aggregation DatabaseOtherSub300G=0.700A=0.300
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.587A=0.413
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs24367283.2E-05alcoholism (heaviness of drinking)21529783

eQTL of rs2436728 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 rs2436728 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 )
chr64031640440316592E067-49009
chr64031670640317926E067-47675
chr64036616340366246E067562
chr64038710940387230E06721508
chr64038758340387949E06721982
chr64038804340388126E06722442
chr64038818840388310E06722587
chr64040480140404952E06839200
chr64038804340388126E06922442
chr64038818840388310E06922587
chr64039301940393315E06927418
chr64039339240393566E06927791
chr64039367640394461E06928075
chr64040451140404785E06938910
chr64040480140404952E06939200
chr64031618540316235E070-49366
chr64031640440316592E070-49009
chr64031670640317926E070-47675
chr64032435240324481E070-41120
chr64032476940324819E070-40782
chr64037748240377926E07011881
chr64037865940378986E07013058
chr64037973140379871E07014130
chr64038097640381510E07015375
chr64038710940387230E07021508
chr64038723240387425E07021631
chr64038758340387949E07021982
chr64038804340388126E07022442
chr64038818840388310E07022587
chr64039301940393315E07027418
chr64039339240393566E07027791
chr64039367640394461E07028075
chr64040451140404785E07038910
chr64040480140404952E07039200
chr64040621440407002E07040613
chr64040727640407467E07041675
chr64040797440408103E07042373
chr64031640440316592E071-49009
chr64031670640317926E071-47675
chr64039301940393315E07127418
chr64039339240393566E07127791
chr64040451140404785E07138910
chr64040480140404952E07139200
chr64031640440316592E072-49009
chr64031670640317926E072-47675
chr64037748240377926E07211881
chr64038758340387949E07221982
chr64039301940393315E07227418
chr64039339240393566E07227791
chr64040480140404952E07239200
chr64031618540316235E073-49366
chr64031640440316592E073-49009
chr64031670640317926E073-47675
chr64036616340366246E073562
chr64038695340387008E07321352
chr64038758340387949E07321982
chr64038804340388126E07322442
chr64038818840388310E07322587
chr64039301940393315E07327418
chr64039339240393566E07327791
chr64039367640394461E07328075
chr64039503940395181E07329438
chr64040480140404952E07339200
chr64040727640407467E07341675
chr64040797440408103E07342373
chr64031640440316592E074-49009
chr64040451140404785E07438910
chr64040480140404952E07439200
chr64031618540316235E081-49366
chr64031640440316592E081-49009
chr64031670640317926E081-47675
chr64036616340366246E081562
chr64037748240377926E08111881
chr64037865940378986E08113058
chr64038620840386258E08120607
chr64038634640386391E08120745
chr64038662940386686E08121028
chr64038695340387008E08121352
chr64038710940387230E08121508
chr64038723240387425E08121631
chr64038758340387949E08121982
chr64038804340388126E08122442
chr64038818840388310E08122587
chr64038974940390239E08124148
chr64039301940393315E08127418
chr64039339240393566E08127791
chr64039367640394461E08128075
chr64039503940395181E08129438
chr64039702140397118E08131420
chr64040451140404785E08138910
chr64040480140404952E08139200
chr64040621440407002E08140613
chr64040727640407467E08141675
chr64040797440408103E08142373
chr64040892040409104E08143319
chr64040927740409395E08143676
chr64031618540316235E082-49366
chr64031640440316592E082-49009
chr64031670640317926E082-47675
chr64035877440358875E082-6726
chr64035897440359132E082-6469
chr64037748240377926E08211881
chr64037865940378986E08213058
chr64037973140379871E08214130
chr64038723240387425E08221631
chr64038758340387949E08221982
chr64038804340388126E08222442
chr64038818840388310E08222587
chr64039301940393315E08227418
chr64039339240393566E08227791
chr64039367640394461E08228075
chr64039503940395181E08229438
chr64040480140404952E08239200
chr64040621440407002E08240613
chr64040727640407467E08241675
chr64040797440408103E08242373
chr64040892040409104E08243319
chr64040927740409395E08243676
chr64041054040410665E08244939
chr64041310140413185E08247500