rs6142970

Homo sapiens
C>T
SS18L1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0092 (2770/29964,GnomAD)
T=0085 (2491/29118,TOPMED)
T=0133 (665/5008,1000G)
T=0061 (235/3854,ALSPAC)
T=0061 (228/3708,TWINSUK)
chr20:62175801 (GRCh38.p7) (20q13.33)
AD
GWASdb2
1   publication(s)
See rs on genome
194 Enhancers around
22 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.62175801C>T
GRCh37.p13 chr 20NC_000020.10:g.60750857C>T
SS18L1 RefSeqGeneNG_034255.1:g.37082C>T

Gene: SS18L1, SS18L1, nBAF chromatin remodeling complex subunit(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SS18L1 transcript variant 2NM_001301778.1:c.N/AIntron Variant
SS18L1 transcript variant 1NM_198935.2:c.N/AIntron Variant
SS18L1 transcript variant 3NR_125980.1:n.N/AIntron Variant
SS18L1 transcript variant 4NR_125981.1:n.N/AIntron Variant
SS18L1 transcript variant X2XM_005260391.1:c.N/AIntron Variant
SS18L1 transcript variant X3XM_011528764.2:c.N/AIntron Variant
SS18L1 transcript variant X6XM_011528767.1:c.N/AIntron Variant
SS18L1 transcript variant X4XM_017027784.1:c.N/AIntron Variant
SS18L1 transcript variant X1XM_005260389.3:c.N/A3 Prime UTR Variant
SS18L1 transcript variant X5XR_001754230.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.863T=0.137
1000GenomesAmericanSub694C=0.960T=0.040
1000GenomesEast AsianSub1008C=0.818T=0.182
1000GenomesEuropeSub1006C=0.943T=0.057
1000GenomesGlobalStudy-wide5008C=0.867T=0.133
1000GenomesSouth AsianSub978C=0.780T=0.220
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.939T=0.061
The Genome Aggregation DatabaseAfricanSub8720C=0.867T=0.133
The Genome Aggregation DatabaseAmericanSub838C=0.940T=0.060
The Genome Aggregation DatabaseEast AsianSub1620C=0.819T=0.181
The Genome Aggregation DatabaseEuropeSub18484C=0.933T=0.066
The Genome Aggregation DatabaseGlobalStudy-wide29964C=0.907T=0.092
The Genome Aggregation DatabaseOtherSub302C=0.880T=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.914T=0.085
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.939T=0.061
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
rs61429700.000104alcohol dependence20201924

eQTL of rs6142970 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 rs6142970 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 )
chr206071539260715442E067-35415
chr206071588060715967E067-34890
chr206071609960716159E067-34698
chr206071620360716340E067-34517
chr206072048560720577E067-30280
chr206072070160720751E067-30106
chr206072075660720865E067-29992
chr206072412160724344E067-26513
chr206072435260725622E067-25235
chr206075955460759672E0678697
chr206078704660787096E06736189
chr206070739960707444E068-43413
chr206070765360707764E068-43093
chr206070786360707928E068-42929
chr206070807060708447E068-42410
chr206070845360708503E068-42354
chr206070867560708729E068-42128
chr206070886260708957E068-41900
chr206070905060709425E068-41432
chr206070944560709671E068-41186
chr206070974360709839E068-41018
chr206071609960716159E068-34698
chr206072070160720751E068-30106
chr206072075660720865E068-29992
chr206072114060721640E068-29217
chr206073182960732463E068-18394
chr206075955460759672E0688697
chr206075977260759826E0688915
chr206078909360789262E06838236
chr206070985360710267E069-40590
chr206071609960716159E069-34698
chr206071620360716340E069-34517
chr206072029060720337E069-30520
chr206072039060720482E069-30375
chr206072048560720577E069-30280
chr206072070160720751E069-30106
chr206072075660720865E069-29992
chr206072114060721640E069-29217
chr206072412160724344E069-26513
chr206072435260725622E069-25235
chr206072581960725977E069-24880
chr206072641360726502E069-24355
chr206073159660731799E069-19058
chr206073182960732463E069-18394
chr206076694460766994E06916087
chr206071620360716340E070-34517
chr206072114060721640E070-29217
chr206072173860721788E070-29069
chr206072195060722004E070-28853
chr206072205860722132E070-28725
chr206072214260722256E070-28601
chr206072232860722465E070-28392
chr206072412160724344E070-26513
chr206072435260725622E070-25235
chr206073124160731537E070-19320
chr206073159660731799E070-19058
chr206073182960732463E070-18394
chr206075955460759672E0708697
chr206075977260759826E0708915
chr206070674660706896E071-43961
chr206070697860707047E071-43810
chr206070717560707338E071-43519
chr206070739960707444E071-43413
chr206070765360707764E071-43093
chr206070786360707928E071-42929
chr206070807060708447E071-42410
chr206070845360708503E071-42354
chr206070867560708729E071-42128
chr206070886260708957E071-41900
chr206070905060709425E071-41432
chr206070944560709671E071-41186
chr206070974360709839E071-41018
chr206070985360710267E071-40590
chr206071579660715876E071-34981
chr206071588060715967E071-34890
chr206071609960716159E071-34698
chr206071620360716340E071-34517
chr206072029060720337E071-30520
chr206072039060720482E071-30375
chr206072048560720577E071-30280
chr206072070160720751E071-30106
chr206072075660720865E071-29992
chr206072272460722768E071-28089
chr206072281360722871E071-27986
chr206072287660722952E071-27905
chr206072295560723005E071-27852
chr206072382760723979E071-26878
chr206072412160724344E071-26513
chr206072435260725622E071-25235
chr206072641360726502E071-24355
chr206073124160731537E071-19320
chr206073159660731799E071-19058
chr206075955460759672E0718697
chr206075977260759826E0718915
chr206078756560787710E07136708
chr206070697860707047E072-43810
chr206070717560707338E072-43519
chr206070739960707444E072-43413
chr206070765360707764E072-43093
chr206070786360707928E072-42929
chr206070807060708447E072-42410
chr206070845360708503E072-42354
chr206070867560708729E072-42128
chr206070886260708957E072-41900
chr206070905060709425E072-41432
chr206070944560709671E072-41186
chr206070974360709839E072-41018
chr206071579660715876E072-34981
chr206071588060715967E072-34890
chr206071609960716159E072-34698
chr206071620360716340E072-34517
chr206072048560720577E072-30280
chr206072070160720751E072-30106
chr206072075660720865E072-29992
chr206072114060721640E072-29217
chr206072412160724344E072-26513
chr206072435260725622E072-25235
chr206072641360726502E072-24355
chr206072669960726776E072-24081
chr206073124160731537E072-19320
chr206073159660731799E072-19058
chr206073470760734862E072-15995
chr206073504760735255E072-15602
chr206075955460759672E0728697
chr206075977260759826E0728915
chr206076694460766994E07216087
chr206076766160767714E07216804
chr206076861960768669E07217762
chr206076869560768745E07217838
chr206070674660706896E073-43961
chr206070697860707047E073-43810
chr206070717560707338E073-43519
chr206070739960707444E073-43413
chr206070765360707764E073-43093
chr206070786360707928E073-42929
chr206070807060708447E073-42410
chr206071563860715725E073-35132
chr206071579660715876E073-34981
chr206071588060715967E073-34890
chr206071609960716159E073-34698
chr206071620360716340E073-34517
chr206072029060720337E073-30520
chr206072039060720482E073-30375
chr206072048560720577E073-30280
chr206072070160720751E073-30106
chr206072075660720865E073-29992
chr206072114060721640E073-29217
chr206072412160724344E073-26513
chr206072435260725622E073-25235
chr206073159660731799E073-19058
chr206073182960732463E073-18394
chr206073252060732570E073-18287
chr206073470760734862E073-15995
chr206073504760735255E073-15602
chr206075955460759672E0738697
chr206075977260759826E0738915
chr206078375260783802E07332895
chr206078382360783971E07332966
chr206070905060709425E074-41432
chr206070944560709671E074-41186
chr206070974360709839E074-41018
chr206070985360710267E074-40590
chr206071609960716159E074-34698
chr206071620360716340E074-34517
chr206072070160720751E074-30106
chr206072075660720865E074-29992
chr206072435260725622E074-25235
chr206075955460759672E0748697
chr206075977260759826E0748915
chr206071609960716159E081-34698
chr206071620360716340E081-34517
chr206072114060721640E081-29217
chr206072173860721788E081-29069
chr206072195060722004E081-28853
chr206072281360722871E081-27986
chr206072287660722952E081-27905
chr206072295560723005E081-27852
chr206072303160723085E081-27772
chr206072319660723246E081-27611
chr206073124160731537E081-19320
chr206073159660731799E081-19058
chr206075955460759672E0818697
chr206075977260759826E0818915
chr206072214260722256E082-28601
chr206072232860722465E082-28392
chr206072272460722768E082-28089
chr206072281360722871E082-27986
chr206072287660722952E082-27905
chr206072295560723005E082-27852
chr206072303160723085E082-27772
chr206072319660723246E082-27611
chr206072382760723979E082-26878
chr206072412160724344E082-26513
chr206072435260725622E082-25235










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr206071640360720289E067-30568
chr206075677360758877E0675916
chr206071640360720289E068-30568
chr206075677360758877E0685916
chr206079378860795098E06842931
chr206071640360720289E069-30568
chr206075677360758877E0695916
chr206079378860795098E06942931
chr206071640360720289E070-30568
chr206075677360758877E0705916
chr206071640360720289E071-30568
chr206075677360758877E0715916
chr206071640360720289E072-30568
chr206075677360758877E0725916
chr206079378860795098E07242931
chr206071640360720289E073-30568
chr206075677360758877E0735916
chr206071640360720289E074-30568
chr206075677360758877E0745916
chr206071640360720289E082-30568
chr206075677360758877E0825916
chr206079378860795098E08242931