rs2296744

Homo sapiens
G>A
LEMD2 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0464 (54634/117644,ExAC)
A=0455 (13634/29918,GnomAD)
A=0412 (12018/29118,TOPMED)
G==0433 (5640/13004,GO-ESP)
A=0485 (2431/5008,1000G)
G==0443 (1706/3854,ALSPAC)
G==0452 (1676/3708,TWINSUK)
chr6:33772605 (GRCh38.p7) (6p21.31)
ND
GWASdb2
1   publication(s)
See rs on genome
248 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.33772605G>A
GRCh37.p13 chr 6NC_000006.11:g.33740382G>A

Gene: LEMD2, LEM domain containing 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LEMD2 transcript variant 2NM_001143944.1:c.N/A3 Prime UTR Variant
LEMD2 transcript variant 1NM_181336.3:c.N/A3 Prime UTR Variant
LEMD2 transcript variant X1XM_017010437.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.827A=0.173
1000GenomesAmericanSub694G=0.560A=0.440
1000GenomesEast AsianSub1008G=0.215A=0.785
1000GenomesEuropeSub1006G=0.501A=0.499
1000GenomesGlobalStudy-wide5008G=0.515A=0.485
1000GenomesSouth AsianSub978G=0.380A=0.620
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.443A=0.557
The Exome Aggregation ConsortiumAmericanSub21598G=0.647A=0.352
The Exome Aggregation ConsortiumAsianSub23350G=0.324A=0.675
The Exome Aggregation ConsortiumEuropeSub71820G=0.455A=0.545
The Exome Aggregation ConsortiumGlobalStudy-wide117644G=0.464A=0.535
The Exome Aggregation ConsortiumOtherSub876G=0.450A=0.550
The Genome Aggregation DatabaseAfricanSub8704G=0.773A=0.227
The Genome Aggregation DatabaseAmericanSub836G=0.500A=0.500
The Genome Aggregation DatabaseEast AsianSub1618G=0.224A=0.776
The Genome Aggregation DatabaseEuropeSub18458G=0.467A=0.532
The Genome Aggregation DatabaseGlobalStudy-wide29918G=0.544A=0.455
The Genome Aggregation DatabaseOtherSub302G=0.480A=0.520
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.587A=0.412
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.452A=0.548
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs22967448.99E-05alcohol and nictotine co-dependence20158304

eQTL of rs2296744 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:33740382LEMD2ENSG00000161904.7G>A3.2975e-7-16531Cerebellum
Chr6:33740382LEMD2ENSG00000161904.7G>A1.6522e-3-16531Frontal_Cortex_BA9
Chr6:33740382LEMD2ENSG00000161904.7G>A9.9739e-5-16531Cortex
Chr6:33740382LEMD2ENSG00000161904.7G>A1.6539e-7-16531Cerebellar_Hemisphere
Chr6:33740382LEMD2ENSG00000161904.7G>A3.0019e-4-16531Caudate_basal_ganglia
Chr6:33740382LEMD2ENSG00000161904.7G>A3.4114e-4-16531Putamen_basal_ganglia
Chr6:33740382LEMD2ENSG00000161904.7G>A2.6947e-6-16531Anterior_cingulate_cortex

meQTL of rs2296744 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 )
chr63370502633705469E067-34913
chr63370551033705661E067-34721
chr63370802033708268E067-32114
chr63370830533708518E067-31864
chr63370855433708879E067-31503
chr63370906933709230E067-31152
chr63371061433710950E067-29432
chr63371110033711171E067-29211
chr63371166633711720E067-28662
chr63373785633740034E067-348
chr63374005033740536E0670
chr63374879033748989E0678408
chr63374900833749959E0678626
chr63375007233750166E0679690
chr63375360533753993E06713223
chr63375438033754424E06713998
chr63375472833754802E06714346
chr63370502633705469E068-34913
chr63370802033708268E068-32114
chr63370830533708518E068-31864
chr63370855433708879E068-31503
chr63370906933709230E068-31152
chr63371061433710950E068-29432
chr63371110033711171E068-29211
chr63371166633711720E068-28662
chr63371278333713016E068-27366
chr63371492633715236E068-25146
chr63371540233715700E068-24682
chr63373785633740034E068-348
chr63374900833749959E0688626
chr63375007233750166E0689690
chr63375360533753993E06813223
chr63375438033754424E06813998
chr63375472833754802E06814346
chr63369843733698772E069-41610
chr63369950433699809E069-40573
chr63369984833699982E069-40400
chr63369998733700906E069-39476
chr63370502633705469E069-34913
chr63370551033705661E069-34721
chr63370802033708268E069-32114
chr63370830533708518E069-31864
chr63371061433710950E069-29432
chr63371110033711171E069-29211
chr63371166633711720E069-28662
chr63371176833712627E069-27755
chr63371540233715700E069-24682
chr63371574533715920E069-24462
chr63372948733729610E069-10772
chr63372985833730254E069-10128
chr63373025633730430E069-9952
chr63373629433736361E069-4021
chr63373636833736766E069-3616
chr63373758233737678E069-2704
chr63373774333737821E069-2561
chr63373785633740034E069-348
chr63375360533753993E06913223
chr63375438033754424E06913998
chr63375472833754802E06914346
chr63378811733788223E06947735
chr63371061433710950E070-29432
chr63371110033711171E070-29211
chr63371176833712627E070-27755
chr63371339633713679E070-26703
chr63373774333737821E070-2561
chr63373785633740034E070-348
chr63374590233746130E0705520
chr63375360533753993E07013223
chr63375438033754424E07013998
chr63375472833754802E07014346
chr63376541733765486E07025035
chr63376555433765604E07025172
chr63376576433765814E07025382
chr63376966333769742E07029281
chr63377033933770542E07029957
chr63377550733775590E07035125
chr63377581433775879E07035432
chr63377628933776339E07035907
chr63378013133780294E07039749
chr63378046633780828E07040084
chr63378103633781146E07040654
chr63378148633781554E07041104
chr63378373433783921E07043352
chr63369106033691172E071-49210
chr63369127533691412E071-48970
chr63369145933692384E071-47998
chr63369843733698772E071-41610
chr63369908333699253E071-41129
chr63369930433699426E071-40956
chr63369950433699809E071-40573
chr63369984833699982E071-40400
chr63369998733700906E071-39476
chr63370502633705469E071-34913
chr63370551033705661E071-34721
chr63370570233706005E071-34377
chr63370802033708268E071-32114
chr63370830533708518E071-31864
chr63370855433708879E071-31503
chr63371061433710950E071-29432
chr63371110033711171E071-29211
chr63371166633711720E071-28662
chr63371176833712627E071-27755
chr63372948733729610E071-10772
chr63372985833730254E071-10128
chr63373629433736361E071-4021
chr63373636833736766E071-3616
chr63373758233737678E071-2704
chr63373774333737821E071-2561
chr63373785633740034E071-348
chr63374005033740536E0710
chr63374053933740828E071157
chr63374090233741035E071520
chr63374126633741348E071884
chr63374144733741501E0711065
chr63374156133741623E0711179
chr63374172633741795E0711344
chr63375360533753993E07113223
chr63375438033754424E07113998
chr63375472833754802E07114346
chr63370502633705469E072-34913
chr63370746733707993E072-32389
chr63370802033708268E072-32114
chr63370830533708518E072-31864
chr63370855433708879E072-31503
chr63371061433710950E072-29432
chr63371110033711171E072-29211
chr63371166633711720E072-28662
chr63371278333713016E072-27366
chr63371492633715236E072-25146
chr63371540233715700E072-24682
chr63371574533715920E072-24462
chr63372948733729610E072-10772
chr63372985833730254E072-10128
chr63373025633730430E072-9952
chr63373063533730790E072-9592
chr63373636833736766E072-3616
chr63373758233737678E072-2704
chr63373774333737821E072-2561
chr63373785633740034E072-348
chr63374005033740536E0720
chr63375360533753993E07213223
chr63375438033754424E07213998
chr63375472833754802E07214346
chr63371061433710950E073-29432
chr63371492633715236E073-25146
chr63371540233715700E073-24682
chr63372948733729610E073-10772
chr63372985833730254E073-10128
chr63373636833736766E073-3616
chr63373774333737821E073-2561
chr63373785633740034E073-348
chr63374005033740536E0730
chr63374053933740828E073157
chr63374090233741035E073520
chr63374807833748160E0737696
chr63375360533753993E07313223
chr63375438033754424E07313998
chr63375472833754802E07314346
chr63369817933698261E074-42121
chr63369826833698322E074-42060
chr63369843733698772E074-41610
chr63369908333699253E074-41129
chr63369930433699426E074-40956
chr63369950433699809E074-40573
chr63369984833699982E074-40400
chr63369998733700906E074-39476
chr63370502633705469E074-34913
chr63370551033705661E074-34721
chr63370570233706005E074-34377
chr63370614033706262E074-34120
chr63370746733707993E074-32389
chr63370802033708268E074-32114
chr63370830533708518E074-31864
chr63370855433708879E074-31503
chr63370906933709230E074-31152
chr63370996833710062E074-30320
chr63371061433710950E074-29432
chr63371110033711171E074-29211
chr63371166633711720E074-28662
chr63371540233715700E074-24682
chr63371574533715920E074-24462
chr63372948733729610E074-10772
chr63372985833730254E074-10128
chr63373025633730430E074-9952
chr63373063533730790E074-9592
chr63373636833736766E074-3616
chr63373785633740034E074-348
chr63375360533753993E07413223
chr63375438033754424E07413998
chr63375472833754802E07414346
chr63369079133690851E081-49531
chr63369106033691172E081-49210
chr63369127533691412E081-48970
chr63369145933692384E081-47998
chr63369246133692617E081-47765
chr63369303533693223E081-47159
chr63369330333693469E081-46913
chr63369381333693885E081-46497
chr63369448633694562E081-45820
chr63369509333695256E081-45126
chr63369567633695960E081-44422
chr63369608533696521E081-43861
chr63369653733696613E081-43769
chr63370746733707993E081-32389
chr63370802033708268E081-32114
chr63370830533708518E081-31864
chr63370855433708879E081-31503
chr63370906933709230E081-31152
chr63370996833710062E081-30320
chr63371061433710950E081-29432
chr63371110033711171E081-29211
chr63371176833712627E081-27755
chr63373736733737417E081-2965
chr63373758233737678E081-2704
chr63373774333737821E081-2561
chr63373785633740034E081-348
chr63374005033740536E0810
chr63374053933740828E081157
chr63374090233741035E081520
chr63374126633741348E081884
chr63375472833754802E08114346
chr63375771233757863E08117330
chr63375787333757975E08117491
chr63376866233768712E08128280
chr63377033933770542E08129957
chr63378013133780294E08139749
chr63378046633780828E08140084
chr63378103633781146E08140654
chr63378148633781554E08141104
chr63369246133692617E082-47765
chr63370132433701379E082-39003
chr63370155233701684E082-38698
chr63370746733707993E082-32389
chr63370802033708268E082-32114
chr63370830533708518E082-31864
chr63370855433708879E082-31503
chr63370906933709230E082-31152
chr63371061433710950E082-29432
chr63371110033711171E082-29211
chr63373629433736361E082-4021
chr63373774333737821E082-2561
chr63373785633740034E082-348
chr63374005033740536E0820
chr63374053933740828E082157
chr63374090233741035E082520
chr63375360533753993E08213223
chr63375438033754424E08213998
chr63375472833754802E08214346










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63375512933757474E06714747
chr63375512933757474E06814747
chr63375512933757474E06914747
chr63375512933757474E07014747
chr63375512933757474E07114747
chr63375512933757474E07214747
chr63375512933757474E07314747
chr63375512933757474E07414747
chr63375512933757474E08114747
chr63375512933757474E08214747