rs4917916

Homo sapiens
G>A
SLF2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0258 (7746/29938,GnomAD)
A=0285 (8308/29118,TOPMED)
A=0361 (1808/5008,1000G)
A=0202 (780/3854,ALSPAC)
A=0209 (776/3708,TWINSUK)
chr10:100913535 (GRCh38.p7) (10q24.31)
AD
GWASdb2
2   publication(s)
See rs on genome
201 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.100913535G>A
GRCh37.p13 chr 10NC_000010.10:g.102673292G>A

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

Molecule type Change Amino acid[Codon] SO Term
SLF2 transcript variant 2NM_001136123.1:c.N/AIntron Variant
SLF2 transcript variant 1NM_018121.3:c.N/AIntron Variant
SLF2 transcript variant 3NM_001243770.1:c.N/A3 Prime UTR Variant
SLF2 transcript variant X1XM_005269965.2:c.N/AIntron Variant
SLF2 transcript variant X2XM_011539944.2:c.N/AIntron Variant
SLF2 transcript variant X3XR_001747138.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.616A=0.384
1000GenomesAmericanSub694G=0.720A=0.280
1000GenomesEast AsianSub1008G=0.453A=0.547
1000GenomesEuropeSub1006G=0.818A=0.182
1000GenomesGlobalStudy-wide5008G=0.639A=0.361
1000GenomesSouth AsianSub978G=0.620A=0.380
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.798A=0.202
The Genome Aggregation DatabaseAfricanSub8704G=0.659A=0.341
The Genome Aggregation DatabaseAmericanSub838G=0.670A=0.330
The Genome Aggregation DatabaseEast AsianSub1608G=0.427A=0.573
The Genome Aggregation DatabaseEuropeSub18486G=0.809A=0.190
The Genome Aggregation DatabaseGlobalStudy-wide29938G=0.741A=0.258
The Genome Aggregation DatabaseOtherSub302G=0.830A=0.170
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.714A=0.285
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.791A=0.209
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
19361613Genetic control of human brain transcript expression in Alzheimer disease.Webster JAAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs49179160.000469alcohol dependence20201924

eQTL of rs4917916 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr10:102673292MRPL43ENSG00000055950.12G>A2.1437e-6-73831Cerebellum
Chr10:102673292MRPL43ENSG00000055950.12G>A5.5041e-5-73831Hypothalamus
Chr10:102673292MRPL43ENSG00000055950.12G>A3.6980e-5-73831Cerebellar_Hemisphere
Chr10:102673292MRPL43ENSG00000055950.12G>A8.3858e-4-73831Caudate_basal_ganglia

meQTL of rs4917916 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 )
chr10102641973102642076E067-31216
chr10102642081102642337E067-30955
chr10102642375102642980E067-30312
chr10102674427102674533E0671135
chr10102674541102674593E0671249
chr10102674968102675018E0671676
chr10102675403102675463E0672111
chr10102676362102676412E0673070
chr10102676481102676628E0673189
chr10102676638102676692E0673346
chr10102676756102676806E0673464
chr10102676818102676872E0673526
chr10102676899102676949E0673607
chr10102677375102677419E0674083
chr10102690202102690318E06716910
chr10102690474102690564E06717182
chr10102691014102691071E06717722
chr10102641397102641817E068-31475
chr10102641845102641937E068-31355
chr10102641973102642076E068-31216
chr10102642081102642337E068-30955
chr10102642375102642980E068-30312
chr10102646354102647408E068-25884
chr10102670160102670220E068-3072
chr10102674968102675018E0681676
chr10102675403102675463E0682111
chr10102676481102676628E0683189
chr10102676638102676692E0683346
chr10102676756102676806E0683464
chr10102683095102683208E0689803
chr10102683392102683573E06810100
chr10102690123102690173E06816831
chr10102690202102690318E06816910
chr10102690474102690564E06817182
chr10102637959102638777E069-34515
chr10102641397102641817E069-31475
chr10102641845102641937E069-31355
chr10102641973102642076E069-31216
chr10102642081102642337E069-30955
chr10102642375102642980E069-30312
chr10102669163102670039E069-3253
chr10102676756102676806E0693464
chr10102676818102676872E0693526
chr10102676899102676949E0693607
chr10102677375102677419E0694083
chr10102683095102683208E0699803
chr10102683392102683573E06910100
chr10102690202102690318E06916910
chr10102690474102690564E06917182
chr10102691014102691071E06917722
chr10102691674102691724E06918382
chr10102691877102691955E06918585
chr10102624864102624981E070-48311
chr10102625008102625104E070-48188
chr10102625107102625176E070-48116
chr10102625394102625491E070-47801
chr10102625830102625912E070-47380
chr10102625922102626068E070-47224
chr10102626147102626313E070-46979
chr10102626883102626956E070-46336
chr10102633572102633682E070-39610
chr10102633856102633953E070-39339
chr10102636401102636468E070-36824
chr10102636472102636612E070-36680
chr10102636620102636782E070-36510
chr10102636860102636914E070-36378
chr10102636965102637655E070-35637
chr10102641845102641937E070-31355
chr10102641973102642076E070-31216
chr10102642081102642337E070-30955
chr10102642375102642980E070-30312
chr10102671405102671458E070-1834
chr10102674427102674533E0701135
chr10102674541102674593E0701249
chr10102637959102638777E071-34515
chr10102640666102641339E071-31953
chr10102641397102641817E071-31475
chr10102641845102641937E071-31355
chr10102641973102642076E071-31216
chr10102642081102642337E071-30955
chr10102642375102642980E071-30312
chr10102649430102649490E071-23802
chr10102669163102670039E071-3253
chr10102674427102674533E0711135
chr10102674541102674593E0711249
chr10102674968102675018E0711676
chr10102675403102675463E0712111
chr10102676481102676628E0713189
chr10102676638102676692E0713346
chr10102676756102676806E0713464
chr10102676818102676872E0713526
chr10102676899102676949E0713607
chr10102683095102683208E0719803
chr10102683392102683573E07110100
chr10102690123102690173E07116831
chr10102690202102690318E07116910
chr10102690474102690564E07117182
chr10102691014102691071E07117722
chr10102691674102691724E07118382
chr10102691877102691955E07118585
chr10102692474102692524E07119182
chr10102624864102624981E072-48311
chr10102625922102626068E072-47224
chr10102626147102626313E072-46979
chr10102637959102638777E072-34515
chr10102641397102641817E072-31475
chr10102641845102641937E072-31355
chr10102641973102642076E072-31216
chr10102642081102642337E072-30955
chr10102642375102642980E072-30312
chr10102675403102675463E0722111
chr10102683095102683208E0729803
chr10102683392102683573E07210100
chr10102690123102690173E07216831
chr10102690202102690318E07216910
chr10102690474102690564E07217182
chr10102691674102691724E07218382
chr10102691877102691955E07218585
chr10102692474102692524E07219182
chr10102641845102641937E073-31355
chr10102641973102642076E073-31216
chr10102642081102642337E073-30955
chr10102642375102642980E073-30312
chr10102674968102675018E0731676
chr10102641397102641817E074-31475
chr10102641845102641937E074-31355
chr10102641973102642076E074-31216
chr10102642081102642337E074-30955
chr10102642375102642980E074-30312
chr10102669163102670039E074-3253
chr10102670160102670220E074-3072
chr10102674427102674533E0741135
chr10102674541102674593E0741249
chr10102674968102675018E0741676
chr10102675403102675463E0742111
chr10102676362102676412E0743070
chr10102676481102676628E0743189
chr10102676638102676692E0743346
chr10102676756102676806E0743464
chr10102676818102676872E0743526
chr10102676899102676949E0743607
chr10102683095102683208E0749803
chr10102683392102683573E07410100
chr10102690123102690173E07416831
chr10102690202102690318E07416910
chr10102690474102690564E07417182
chr10102691014102691071E07417722
chr10102691674102691724E07418382
chr10102691877102691955E07418585
chr10102692474102692524E07419182
chr10102623361102623411E081-49881
chr10102623445102623598E081-49694
chr10102623830102624135E081-49157
chr10102624201102624838E081-48454
chr10102624864102624981E081-48311
chr10102625008102625104E081-48188
chr10102625107102625176E081-48116
chr10102625394102625491E081-47801
chr10102625638102625723E081-47569
chr10102625830102625912E081-47380
chr10102625922102626068E081-47224
chr10102626147102626313E081-46979
chr10102626883102626956E081-46336
chr10102628274102628740E081-44552
chr10102628745102628870E081-44422
chr10102633572102633682E081-39610
chr10102633856102633953E081-39339
chr10102641845102641937E081-31355
chr10102641973102642076E081-31216
chr10102642081102642337E081-30955
chr10102642375102642980E081-30312
chr10102670374102670434E081-2858
chr10102670442102670575E081-2717
chr10102670652102670749E081-2543
chr10102670828102670878E081-2414
chr10102670906102670971E081-2321
chr10102671126102671176E081-2116
chr10102671203102671363E081-1929
chr10102671405102671458E081-1834
chr10102674427102674533E0811135
chr10102674541102674593E0811249
chr10102623361102623411E082-49881
chr10102623445102623598E082-49694
chr10102623830102624135E082-49157
chr10102624201102624838E082-48454
chr10102624864102624981E082-48311
chr10102625008102625104E082-48188
chr10102625107102625176E082-48116
chr10102625394102625491E082-47801
chr10102625638102625723E082-47569
chr10102625830102625912E082-47380
chr10102625922102626068E082-47224
chr10102626883102626956E082-46336
chr10102636472102636612E082-36680
chr10102636620102636782E082-36510
chr10102636860102636914E082-36378
chr10102636965102637655E082-35637
chr10102641845102641937E082-31355
chr10102641973102642076E082-31216
chr10102642081102642337E082-30955
chr10102642375102642980E082-30312










Promoter Annotation (GRCh37.p13)

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