rs3802724

Homo sapiens
T>C
SLF2 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0259 (7740/29830,GnomAD)
C=0285 (8312/29118,TOPMED)
C=0361 (1807/5008,1000G)
C=0202 (780/3854,ALSPAC)
C=0210 (778/3708,TWINSUK)
chr10:100912961 (GRCh38.p7) (10q24.31)
AD
GWASdb2
1   publication(s)
See rs on genome
203 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.100912961T>C
GRCh37.p13 chr 10NC_000010.10:g.102672718T>C

Gene: SLF2, SMC5-SMC6 complex localization factor 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SLF2 transcript variant 1NM_018121.3:c.N/A5 Prime UTR Variant
SLF2 transcript variant 2NM_001136123.1:c.N/A5 Prime UTR Variant
SLF2 transcript variant 3NM_001243770.1:c.N/A5 Prime UTR Variant
SLF2 transcript variant X1XM_005269965.2:c.N/A5 Prime UTR Variant
SLF2 transcript variant X2XM_011539944.2:c.N/A5 Prime UTR Variant
SLF2 transcript variant X3XR_001747138.1:n....XR_001747138.1:n.10T>CT>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.616C=0.384
1000GenomesAmericanSub694T=0.720C=0.280
1000GenomesEast AsianSub1008T=0.455C=0.545
1000GenomesEuropeSub1006T=0.817C=0.183
1000GenomesGlobalStudy-wide5008T=0.639C=0.361
1000GenomesSouth AsianSub978T=0.620C=0.380
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.798C=0.202
The Genome Aggregation DatabaseAfricanSub8682T=0.658C=0.342
The Genome Aggregation DatabaseAmericanSub838T=0.670C=0.330
The Genome Aggregation DatabaseEast AsianSub1608T=0.423C=0.577
The Genome Aggregation DatabaseEuropeSub18402T=0.808C=0.191
The Genome Aggregation DatabaseGlobalStudy-wide29830T=0.740C=0.259
The Genome Aggregation DatabaseOtherSub300T=0.830C=0.170
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.714C=0.285
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.790C=0.210
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs38027240.000337alcohol dependence20201924

eQTL of rs3802724 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr10:102672718MRPL43ENSG00000055950.12T>C2.1437e-6-74405Cerebellum
Chr10:102672718MRPL43ENSG00000055950.12T>C5.5041e-5-74405Hypothalamus
Chr10:102672718MRPL43ENSG00000055950.12T>C3.6980e-5-74405Cerebellar_Hemisphere
Chr10:102672718MRPL43ENSG00000055950.12T>C8.3858e-4-74405Caudate_basal_ganglia

meQTL of rs3802724 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 )
chr10102641973102642076E067-30642
chr10102642081102642337E067-30381
chr10102642375102642980E067-29738
chr10102674427102674533E0671709
chr10102674541102674593E0671823
chr10102674968102675018E0672250
chr10102675403102675463E0672685
chr10102676362102676412E0673644
chr10102676481102676628E0673763
chr10102676638102676692E0673920
chr10102676756102676806E0674038
chr10102676818102676872E0674100
chr10102676899102676949E0674181
chr10102677375102677419E0674657
chr10102690202102690318E06717484
chr10102690474102690564E06717756
chr10102691014102691071E06718296
chr10102641397102641817E068-30901
chr10102641845102641937E068-30781
chr10102641973102642076E068-30642
chr10102642081102642337E068-30381
chr10102642375102642980E068-29738
chr10102646354102647408E068-25310
chr10102670160102670220E068-2498
chr10102674968102675018E0682250
chr10102675403102675463E0682685
chr10102676481102676628E0683763
chr10102676638102676692E0683920
chr10102676756102676806E0684038
chr10102683095102683208E06810377
chr10102683392102683573E06810674
chr10102690123102690173E06817405
chr10102690202102690318E06817484
chr10102690474102690564E06817756
chr10102637959102638777E069-33941
chr10102641397102641817E069-30901
chr10102641845102641937E069-30781
chr10102641973102642076E069-30642
chr10102642081102642337E069-30381
chr10102642375102642980E069-29738
chr10102669163102670039E069-2679
chr10102676756102676806E0694038
chr10102676818102676872E0694100
chr10102676899102676949E0694181
chr10102677375102677419E0694657
chr10102683095102683208E06910377
chr10102683392102683573E06910674
chr10102690202102690318E06917484
chr10102690474102690564E06917756
chr10102691014102691071E06918296
chr10102691674102691724E06918956
chr10102691877102691955E06919159
chr10102624864102624981E070-47737
chr10102625008102625104E070-47614
chr10102625107102625176E070-47542
chr10102625394102625491E070-47227
chr10102625830102625912E070-46806
chr10102625922102626068E070-46650
chr10102626147102626313E070-46405
chr10102626883102626956E070-45762
chr10102633572102633682E070-39036
chr10102633856102633953E070-38765
chr10102636401102636468E070-36250
chr10102636472102636612E070-36106
chr10102636620102636782E070-35936
chr10102636860102636914E070-35804
chr10102636965102637655E070-35063
chr10102641845102641937E070-30781
chr10102641973102642076E070-30642
chr10102642081102642337E070-30381
chr10102642375102642980E070-29738
chr10102671405102671458E070-1260
chr10102674427102674533E0701709
chr10102674541102674593E0701823
chr10102637959102638777E071-33941
chr10102640666102641339E071-31379
chr10102641397102641817E071-30901
chr10102641845102641937E071-30781
chr10102641973102642076E071-30642
chr10102642081102642337E071-30381
chr10102642375102642980E071-29738
chr10102649430102649490E071-23228
chr10102669163102670039E071-2679
chr10102674427102674533E0711709
chr10102674541102674593E0711823
chr10102674968102675018E0712250
chr10102675403102675463E0712685
chr10102676481102676628E0713763
chr10102676638102676692E0713920
chr10102676756102676806E0714038
chr10102676818102676872E0714100
chr10102676899102676949E0714181
chr10102683095102683208E07110377
chr10102683392102683573E07110674
chr10102690123102690173E07117405
chr10102690202102690318E07117484
chr10102690474102690564E07117756
chr10102691014102691071E07118296
chr10102691674102691724E07118956
chr10102691877102691955E07119159
chr10102692474102692524E07119756
chr10102624864102624981E072-47737
chr10102625922102626068E072-46650
chr10102626147102626313E072-46405
chr10102637959102638777E072-33941
chr10102641397102641817E072-30901
chr10102641845102641937E072-30781
chr10102641973102642076E072-30642
chr10102642081102642337E072-30381
chr10102642375102642980E072-29738
chr10102675403102675463E0722685
chr10102683095102683208E07210377
chr10102683392102683573E07210674
chr10102690123102690173E07217405
chr10102690202102690318E07217484
chr10102690474102690564E07217756
chr10102691674102691724E07218956
chr10102691877102691955E07219159
chr10102692474102692524E07219756
chr10102641845102641937E073-30781
chr10102641973102642076E073-30642
chr10102642081102642337E073-30381
chr10102642375102642980E073-29738
chr10102674968102675018E0732250
chr10102641397102641817E074-30901
chr10102641845102641937E074-30781
chr10102641973102642076E074-30642
chr10102642081102642337E074-30381
chr10102642375102642980E074-29738
chr10102669163102670039E074-2679
chr10102670160102670220E074-2498
chr10102674427102674533E0741709
chr10102674541102674593E0741823
chr10102674968102675018E0742250
chr10102675403102675463E0742685
chr10102676362102676412E0743644
chr10102676481102676628E0743763
chr10102676638102676692E0743920
chr10102676756102676806E0744038
chr10102676818102676872E0744100
chr10102676899102676949E0744181
chr10102683095102683208E07410377
chr10102683392102683573E07410674
chr10102690123102690173E07417405
chr10102690202102690318E07417484
chr10102690474102690564E07417756
chr10102691014102691071E07418296
chr10102691674102691724E07418956
chr10102691877102691955E07419159
chr10102692474102692524E07419756
chr10102622918102623042E081-49676
chr10102623053102623151E081-49567
chr10102623361102623411E081-49307
chr10102623445102623598E081-49120
chr10102623830102624135E081-48583
chr10102624201102624838E081-47880
chr10102624864102624981E081-47737
chr10102625008102625104E081-47614
chr10102625107102625176E081-47542
chr10102625394102625491E081-47227
chr10102625638102625723E081-46995
chr10102625830102625912E081-46806
chr10102625922102626068E081-46650
chr10102626147102626313E081-46405
chr10102626883102626956E081-45762
chr10102628274102628740E081-43978
chr10102628745102628870E081-43848
chr10102633572102633682E081-39036
chr10102633856102633953E081-38765
chr10102641845102641937E081-30781
chr10102641973102642076E081-30642
chr10102642081102642337E081-30381
chr10102642375102642980E081-29738
chr10102670374102670434E081-2284
chr10102670442102670575E081-2143
chr10102670652102670749E081-1969
chr10102670828102670878E081-1840
chr10102670906102670971E081-1747
chr10102671126102671176E081-1542
chr10102671203102671363E081-1355
chr10102671405102671458E081-1260
chr10102674427102674533E0811709
chr10102674541102674593E0811823
chr10102623361102623411E082-49307
chr10102623445102623598E082-49120
chr10102623830102624135E082-48583
chr10102624201102624838E082-47880
chr10102624864102624981E082-47737
chr10102625008102625104E082-47614
chr10102625107102625176E082-47542
chr10102625394102625491E082-47227
chr10102625638102625723E082-46995
chr10102625830102625912E082-46806
chr10102625922102626068E082-46650
chr10102626883102626956E082-45762
chr10102636472102636612E082-36106
chr10102636620102636782E082-35936
chr10102636860102636914E082-35804
chr10102636965102637655E082-35063
chr10102641845102641937E082-30781
chr10102641973102642076E082-30642
chr10102642081102642337E082-30381
chr10102642375102642980E082-29738










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr10102671564102673803E0670
chr10102671564102673803E0680
chr10102671564102673803E0690
chr10102671564102673803E0700
chr10102671564102673803E0710
chr10102671564102673803E0720
chr10102671564102673803E0730
chr10102671564102673803E0740
chr10102671564102673803E0810
chr10102671564102673803E0820