rs6142969

Homo sapiens
C>T
SS18L1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0092 (2766/29940,GnomAD)
T=0085 (2501/29118,TOPMED)
T=0133 (666/5008,1000G)
T=0061 (235/3854,ALSPAC)
T=0061 (227/3708,TWINSUK)
chr20:62174127 (GRCh38.p7) (20q13.33)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.62174127C>T
GRCh37.p13 chr 20NC_000020.10:g.60749183C>T
SS18L1 RefSeqGeneNG_034255.1:g.35408C>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 X1XM_005260389.3:c.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 X5XR_001754230.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.862T=0.138
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 DatabaseAfricanSub8714C=0.867T=0.133
The Genome Aggregation DatabaseAmericanSub838C=0.940T=0.060
The Genome Aggregation DatabaseEast AsianSub1612C=0.819T=0.181
The Genome Aggregation DatabaseEuropeSub18474C=0.933T=0.066
The Genome Aggregation DatabaseGlobalStudy-wide29940C=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
rs61429690.000278alcohol dependence20201924

eQTL of rs6142969 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 rs6142969 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 )
chr206069950860699722E067-49461
chr206069984360699932E067-49251
chr206069996960700019E067-49164
chr206070031060700390E067-48793
chr206071539260715442E067-33741
chr206071588060715967E067-33216
chr206071609960716159E067-33024
chr206071620360716340E067-32843
chr206072048560720577E067-28606
chr206072070160720751E067-28432
chr206072075660720865E067-28318
chr206072412160724344E067-24839
chr206072435260725622E067-23561
chr206075955460759672E06710371
chr206078704660787096E06737863
chr206070739960707444E068-41739
chr206070765360707764E068-41419
chr206070786360707928E068-41255
chr206070807060708447E068-40736
chr206070845360708503E068-40680
chr206070867560708729E068-40454
chr206070886260708957E068-40226
chr206070905060709425E068-39758
chr206070944560709671E068-39512
chr206070974360709839E068-39344
chr206071609960716159E068-33024
chr206072070160720751E068-28432
chr206072075660720865E068-28318
chr206072114060721640E068-27543
chr206073182960732463E068-16720
chr206075955460759672E06810371
chr206075977260759826E06810589
chr206078909360789262E06839910
chr206069950860699722E069-49461
chr206069984360699932E069-49251
chr206069996960700019E069-49164
chr206070985360710267E069-38916
chr206071609960716159E069-33024
chr206071620360716340E069-32843
chr206072029060720337E069-28846
chr206072039060720482E069-28701
chr206072048560720577E069-28606
chr206072070160720751E069-28432
chr206072075660720865E069-28318
chr206072114060721640E069-27543
chr206072412160724344E069-24839
chr206072435260725622E069-23561
chr206072581960725977E069-23206
chr206072641360726502E069-22681
chr206073159660731799E069-17384
chr206073182960732463E069-16720
chr206076694460766994E06917761
chr206071620360716340E070-32843
chr206072114060721640E070-27543
chr206072173860721788E070-27395
chr206072195060722004E070-27179
chr206072205860722132E070-27051
chr206072214260722256E070-26927
chr206072232860722465E070-26718
chr206072412160724344E070-24839
chr206072435260725622E070-23561
chr206073124160731537E070-17646
chr206073159660731799E070-17384
chr206073182960732463E070-16720
chr206075955460759672E07010371
chr206075977260759826E07010589
chr206069984360699932E071-49251
chr206069996960700019E071-49164
chr206070674660706896E071-42287
chr206070697860707047E071-42136
chr206070717560707338E071-41845
chr206070739960707444E071-41739
chr206070765360707764E071-41419
chr206070786360707928E071-41255
chr206070807060708447E071-40736
chr206070845360708503E071-40680
chr206070867560708729E071-40454
chr206070886260708957E071-40226
chr206070905060709425E071-39758
chr206070944560709671E071-39512
chr206070974360709839E071-39344
chr206070985360710267E071-38916
chr206071579660715876E071-33307
chr206071588060715967E071-33216
chr206071609960716159E071-33024
chr206071620360716340E071-32843
chr206072029060720337E071-28846
chr206072039060720482E071-28701
chr206072048560720577E071-28606
chr206072070160720751E071-28432
chr206072075660720865E071-28318
chr206072272460722768E071-26415
chr206072281360722871E071-26312
chr206072287660722952E071-26231
chr206072295560723005E071-26178
chr206072382760723979E071-25204
chr206072412160724344E071-24839
chr206072435260725622E071-23561
chr206072641360726502E071-22681
chr206073124160731537E071-17646
chr206073159660731799E071-17384
chr206075955460759672E07110371
chr206075977260759826E07110589
chr206078756560787710E07138382
chr206069950860699722E072-49461
chr206069984360699932E072-49251
chr206069996960700019E072-49164
chr206070031060700390E072-48793
chr206070697860707047E072-42136
chr206070717560707338E072-41845
chr206070739960707444E072-41739
chr206070765360707764E072-41419
chr206070786360707928E072-41255
chr206070807060708447E072-40736
chr206070845360708503E072-40680
chr206070867560708729E072-40454
chr206070886260708957E072-40226
chr206070905060709425E072-39758
chr206070944560709671E072-39512
chr206070974360709839E072-39344
chr206071579660715876E072-33307
chr206071588060715967E072-33216
chr206071609960716159E072-33024
chr206071620360716340E072-32843
chr206072048560720577E072-28606
chr206072070160720751E072-28432
chr206072075660720865E072-28318
chr206072114060721640E072-27543
chr206072412160724344E072-24839
chr206072435260725622E072-23561
chr206072641360726502E072-22681
chr206072669960726776E072-22407
chr206073124160731537E072-17646
chr206073159660731799E072-17384
chr206073470760734862E072-14321
chr206073504760735255E072-13928
chr206075955460759672E07210371
chr206075977260759826E07210589
chr206076694460766994E07217761
chr206076766160767714E07218478
chr206076861960768669E07219436
chr206076869560768745E07219512
chr206069984360699932E073-49251
chr206069996960700019E073-49164
chr206070674660706896E073-42287
chr206070697860707047E073-42136
chr206070717560707338E073-41845
chr206070739960707444E073-41739
chr206070765360707764E073-41419
chr206070786360707928E073-41255
chr206070807060708447E073-40736
chr206071563860715725E073-33458
chr206071579660715876E073-33307
chr206071588060715967E073-33216
chr206071609960716159E073-33024
chr206071620360716340E073-32843
chr206072029060720337E073-28846
chr206072039060720482E073-28701
chr206072048560720577E073-28606
chr206072070160720751E073-28432
chr206072075660720865E073-28318
chr206072114060721640E073-27543
chr206072412160724344E073-24839
chr206072435260725622E073-23561
chr206073159660731799E073-17384
chr206073182960732463E073-16720
chr206073252060732570E073-16613
chr206073470760734862E073-14321
chr206073504760735255E073-13928
chr206075955460759672E07310371
chr206075977260759826E07310589
chr206078375260783802E07334569
chr206078382360783971E07334640
chr206069950860699722E074-49461
chr206070905060709425E074-39758
chr206070944560709671E074-39512
chr206070974360709839E074-39344
chr206070985360710267E074-38916
chr206071609960716159E074-33024
chr206071620360716340E074-32843
chr206072070160720751E074-28432
chr206072075660720865E074-28318
chr206072435260725622E074-23561
chr206075955460759672E07410371
chr206075977260759826E07410589
chr206069950860699722E081-49461
chr206069984360699932E081-49251
chr206069996960700019E081-49164
chr206070031060700390E081-48793
chr206071609960716159E081-33024
chr206071620360716340E081-32843
chr206072114060721640E081-27543
chr206072173860721788E081-27395
chr206072195060722004E081-27179
chr206072281360722871E081-26312
chr206072287660722952E081-26231
chr206072295560723005E081-26178
chr206072303160723085E081-26098
chr206072319660723246E081-25937
chr206073124160731537E081-17646
chr206073159660731799E081-17384
chr206075955460759672E08110371
chr206075977260759826E08110589
chr206069984360699932E082-49251
chr206069996960700019E082-49164
chr206070031060700390E082-48793
chr206072214260722256E082-26927
chr206072232860722465E082-26718
chr206072272460722768E082-26415
chr206072281360722871E082-26312
chr206072287660722952E082-26231
chr206072295560723005E082-26178
chr206072303160723085E082-26098
chr206072319660723246E082-25937
chr206072382760723979E082-25204
chr206072412160724344E082-24839
chr206072435260725622E082-23561










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr206071640360720289E067-28894
chr206075677360758877E0677590
chr206071640360720289E068-28894
chr206075677360758877E0687590
chr206079378860795098E06844605
chr206071640360720289E069-28894
chr206075677360758877E0697590
chr206079378860795098E06944605
chr206071640360720289E070-28894
chr206075677360758877E0707590
chr206071640360720289E071-28894
chr206075677360758877E0717590
chr206071640360720289E072-28894
chr206075677360758877E0727590
chr206079378860795098E07244605
chr206071640360720289E073-28894
chr206075677360758877E0737590
chr206071640360720289E074-28894
chr206075677360758877E0747590
chr206071640360720289E082-28894
chr206075677360758877E0827590
chr206079378860795098E08244605