rs12241232

Homo sapiens
T>C
SLF2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0264 (7741/29320,GnomAD)
C=0285 (8301/29118,TOPMED)
C=0361 (1807/5008,1000G)
C=0203 (783/3854,ALSPAC)
C=0210 (777/3708,TWINSUK)
chr10:100932847 (GRCh38.p7) (10q24.31)
AD
GWASdb2
3   publication(s)
See rs on genome
115 Enhancers around
12 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.100932847T>C
GRCh37.p13 chr 10NC_000010.10:g.102692604T>C

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/AGenic Downstream Transcript 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
1000GenomesAfricanSub1322T=0.616C=0.384
1000GenomesAmericanSub694T=0.720C=0.280
1000GenomesEast AsianSub1008T=0.454C=0.546
1000GenomesEuropeSub1006T=0.818C=0.182
1000GenomesGlobalStudy-wide5008T=0.639C=0.361
1000GenomesSouth AsianSub978T=0.620C=0.380
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.797C=0.203
The Genome Aggregation DatabaseAfricanSub8656T=0.658C=0.342
The Genome Aggregation DatabaseAmericanSub828T=0.660C=0.340
The Genome Aggregation DatabaseEast AsianSub1606T=0.422C=0.578
The Genome Aggregation DatabaseEuropeSub17930T=0.803C=0.196
The Genome Aggregation DatabaseGlobalStudy-wide29320T=0.736C=0.264
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
19128478Complex nature of SNP genotype effects on gene expression in primary human leucocytes.Heap GABMC Med Genomics
19680542Tissue effect on genetic control of transcript isoform variation.Kwan TPLoS Genet

P-Value

SNP ID p-value Traits Study
rs122412320.000489alcohol dependence20201924

eQTL of rs12241232 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr10:102692604MRPL43ENSG00000055950.12T>C2.1437e-6-54519Cerebellum
Chr10:102692604MRPL43ENSG00000055950.12T>C5.5041e-5-54519Hypothalamus
Chr10:102692604MRPL43ENSG00000055950.12T>C3.6980e-5-54519Cerebellar_Hemisphere
Chr10:102692604MRPL43ENSG00000055950.12T>C8.3858e-4-54519Caudate_basal_ganglia

meQTL of rs12241232 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 )
chr10102674427102674533E067-18071
chr10102674541102674593E067-18011
chr10102674968102675018E067-17586
chr10102675403102675463E067-17141
chr10102676362102676412E067-16192
chr10102676481102676628E067-15976
chr10102676638102676692E067-15912
chr10102676756102676806E067-15798
chr10102676818102676872E067-15732
chr10102676899102676949E067-15655
chr10102677375102677419E067-15185
chr10102690202102690318E067-2286
chr10102690474102690564E067-2040
chr10102691014102691071E067-1533
chr10102728355102728532E06735751
chr10102646354102647408E068-45196
chr10102670160102670220E068-22384
chr10102674968102675018E068-17586
chr10102675403102675463E068-17141
chr10102676481102676628E068-15976
chr10102676638102676692E068-15912
chr10102676756102676806E068-15798
chr10102683095102683208E068-9396
chr10102683392102683573E068-9031
chr10102690123102690173E068-2431
chr10102690202102690318E068-2286
chr10102690474102690564E068-2040
chr10102728355102728532E06835751
chr10102669163102670039E069-22565
chr10102676756102676806E069-15798
chr10102676818102676872E069-15732
chr10102676899102676949E069-15655
chr10102677375102677419E069-15185
chr10102683095102683208E069-9396
chr10102683392102683573E069-9031
chr10102690202102690318E069-2286
chr10102690474102690564E069-2040
chr10102691014102691071E069-1533
chr10102691674102691724E069-880
chr10102691877102691955E069-649
chr10102727954102728353E06935350
chr10102728355102728532E06935751
chr10102671405102671458E070-21146
chr10102674427102674533E070-18071
chr10102674541102674593E070-18011
chr10102649430102649490E071-43114
chr10102669163102670039E071-22565
chr10102674427102674533E071-18071
chr10102674541102674593E071-18011
chr10102674968102675018E071-17586
chr10102675403102675463E071-17141
chr10102676481102676628E071-15976
chr10102676638102676692E071-15912
chr10102676756102676806E071-15798
chr10102676818102676872E071-15732
chr10102676899102676949E071-15655
chr10102683095102683208E071-9396
chr10102683392102683573E071-9031
chr10102690123102690173E071-2431
chr10102690202102690318E071-2286
chr10102690474102690564E071-2040
chr10102691014102691071E071-1533
chr10102691674102691724E071-880
chr10102691877102691955E071-649
chr10102692474102692524E071-80
chr10102727954102728353E07135350
chr10102728355102728532E07135751
chr10102675403102675463E072-17141
chr10102683095102683208E072-9396
chr10102683392102683573E072-9031
chr10102690123102690173E072-2431
chr10102690202102690318E072-2286
chr10102690474102690564E072-2040
chr10102691674102691724E072-880
chr10102691877102691955E072-649
chr10102692474102692524E072-80
chr10102728355102728532E07235751
chr10102674968102675018E073-17586
chr10102728355102728532E07335751
chr10102669163102670039E074-22565
chr10102670160102670220E074-22384
chr10102674427102674533E074-18071
chr10102674541102674593E074-18011
chr10102674968102675018E074-17586
chr10102675403102675463E074-17141
chr10102676362102676412E074-16192
chr10102676481102676628E074-15976
chr10102676638102676692E074-15912
chr10102676756102676806E074-15798
chr10102676818102676872E074-15732
chr10102676899102676949E074-15655
chr10102683095102683208E074-9396
chr10102683392102683573E074-9031
chr10102690123102690173E074-2431
chr10102690202102690318E074-2286
chr10102690474102690564E074-2040
chr10102691014102691071E074-1533
chr10102691674102691724E074-880
chr10102691877102691955E074-649
chr10102692474102692524E074-80
chr10102728355102728532E07435751
chr10102670374102670434E081-22170
chr10102670442102670575E081-22029
chr10102670652102670749E081-21855
chr10102670828102670878E081-21726
chr10102670906102670971E081-21633
chr10102671126102671176E081-21428
chr10102671203102671363E081-21241
chr10102671405102671458E081-21146
chr10102674427102674533E081-18071
chr10102674541102674593E081-18011
chr10102727791102727838E08135187
chr10102727954102728353E08135350
chr10102728355102728532E08135751
chr10102727791102727838E08235187










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr10102671564102673803E067-18801
chr10102671564102673803E068-18801
chr10102671564102673803E069-18801
chr10102671564102673803E070-18801
chr10102671564102673803E071-18801
chr10102671564102673803E072-18801
chr10102671564102673803E073-18801
chr10102728545102731770E07335941
chr10102671564102673803E074-18801
chr10102671564102673803E081-18801
chr10102671564102673803E082-18801
chr10102728545102731770E08235941