rs3764198

Homo sapiens
C>A / C>T
LINS1 : Splice Donor Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0143 (4308/29972,GnomAD)
C==0147 (4299/29118,TOPMED)
C==0250 (1251/5008,1000G)
C==0090 (345/3854,ALSPAC)
C==0092 (340/3708,TWINSUK)
chr15:100570360 (GRCh38.p7) (15q26.3)
AD
GWASdb2
1   publication(s)
See rs on genome
168 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.100570360C>A
GRCh38.p7 chr 15NC_000015.10:g.100570360C>T
GRCh37.p13 chr 15NC_000015.9:g.101110565C>A
GRCh37.p13 chr 15NC_000015.9:g.101110565C>T
LINS1 RefSeqGeneNG_034076.1:g.36881G>T
LINS1 RefSeqGeneNG_034076.1:g.36881G>A

Gene: LINS1, lines homolog 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINS1 transcript variant 1NM_001040616.2:c.N/AIntron Variant
LINS1 transcript variant X1XM_005254941.1:c.N/AIntron Variant
LINS1 transcript variant X2XM_005254943.1:c.N/AIntron Variant
LINS1 transcript variant X3XM_017022398.1:c.N/AIntron Variant
LINS1 transcript variant X4XM_017022399.1:c.N/AIntron Variant
LINS1 transcript variant X7XM_017022400.1:c.N/AIntron Variant
LINS1 transcript variant X5XR_001751346.1:n.N/ASplice Donor Variant
LINS1 transcript variant X11XR_001751348.1:n.N/ASplice Donor Variant
LINS1 transcript variant X9XR_001751347.1:n.N/AIntron Variant
LINS1 transcript variant X10XR_243210.3:n.N/AIntron Variant
LINS1 transcript variant X12XR_429464.3:n.N/AIntron Variant
LINS1 transcript variant X6XR_931862.2:n.N/AIntron Variant
LINS1 transcript variant X8XR_931863.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.188T=0.812
1000GenomesAmericanSub694C=0.220T=0.780
1000GenomesEast AsianSub1008C=0.612T=0.388
1000GenomesEuropeSub1006C=0.087T=0.913
1000GenomesGlobalStudy-wide5008C=0.250T=0.750
1000GenomesSouth AsianSub978C=0.150T=0.850
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.090T=0.910
The Genome Aggregation DatabaseAfricanSub8724C=0.163T=0.836
The Genome Aggregation DatabaseAmericanSub834C=0.190T=0.81,
The Genome Aggregation DatabaseEast AsianSub1614C=0.672T=0.328
The Genome Aggregation DatabaseEuropeSub18498C=0.085T=0.915
The Genome Aggregation DatabaseGlobalStudy-wide29972C=0.143T=0.855
The Genome Aggregation DatabaseOtherSub302C=0.250T=0.75,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.147T=0.852
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.092T=0.908
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
rs37641980.00093alcohol dependence20201924

eQTL of rs3764198 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:101110565CERS3ENSG00000154227.9C>T6.3302e-1125365Cerebellum
Chr15:101110565CERS3ENSG00000154227.9C>T1.4305e-925365Cerebellar_Hemisphere

meQTL of rs3764198 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 )
chr154288296142883026E067-47290
chr154288318542883239E067-47077
chr154288334242883408E067-46908
chr154288354142883634E067-46682
chr154288368442884064E067-46252
chr154288645042886677E067-43639
chr154288773642888439E067-41877
chr154288866742888774E067-41542
chr154290104342901266E067-29050
chr154290130542901577E067-28739
chr154296478842964838E06734472
chr154296980142969851E06739485
chr154297004242970317E06739726
chr154297053242970634E06740216
chr154297067042970996E06740354
chr154297120242971256E06740886
chr154297127042971405E06740954
chr154297141042971764E06741094
chr154288318542883239E068-47077
chr154288334242883408E068-46908
chr154288354142883634E068-46682
chr154288368442884064E068-46252
chr154288414142884191E068-46125
chr154288426342884384E068-45932
chr154288631742886417E068-43899
chr154288645042886677E068-43639
chr154288681342886867E068-43449
chr154288712042887170E068-43146
chr154288756642887719E068-42597
chr154288773642888439E068-41877
chr154288866742888774E068-41542
chr154289687942897028E068-33288
chr154289717542898656E068-31660
chr154289999142901034E068-29282
chr154290104342901266E068-29050
chr154290130542901577E068-28739
chr154296359042963964E06833274
chr154296406642964177E06833750
chr154296431042964461E06833994
chr154296980142969851E06839485
chr154297004242970317E06839726
chr154288058742880819E069-49497
chr154288296142883026E069-47290
chr154288318542883239E069-47077
chr154288334242883408E069-46908
chr154288354142883634E069-46682
chr154288368442884064E069-46252
chr154288712042887170E069-43146
chr154288756642887719E069-42597
chr154288773642888439E069-41877
chr154288866742888774E069-41542
chr154288880842888876E069-41440
chr154288917442889242E069-41074
chr154289717542898656E069-31660
chr154289999142901034E069-29282
chr154290104342901266E069-29050
chr154290130542901577E069-28739
chr154291610242916152E069-14164
chr154291622842916289E069-14027
chr154291630042916350E069-13966
chr154293911942939169E0698803
chr154296431042964461E06933994
chr154296478842964838E06934472
chr154296980142969851E06939485
chr154297004242970317E06939726
chr154297053242970634E06940216
chr154297067042970996E06940354
chr154297120242971256E06940886
chr154297127042971405E06940954
chr154297141042971764E06941094
chr154288624242886302E070-44014
chr154288631742886417E070-43899
chr154288645042886677E070-43639
chr154288756642887719E070-42597
chr154288296142883026E071-47290
chr154288318542883239E071-47077
chr154288334242883408E071-46908
chr154288354142883634E071-46682
chr154288712042887170E071-43146
chr154288756642887719E071-42597
chr154288773642888439E071-41877
chr154288866742888774E071-41542
chr154288880842888876E071-41440
chr154289687942897028E071-33288
chr154289717542898656E071-31660
chr154289999142901034E071-29282
chr154290104342901266E071-29050
chr154290130542901577E071-28739
chr154293911942939169E0718803
chr154296406642964177E07133750
chr154296431042964461E07133994
chr154296478842964838E07134472
chr154296980142969851E07139485
chr154297004242970317E07139726
chr154297053242970634E07140216
chr154297067042970996E07140354
chr154297120242971256E07140886
chr154297127042971405E07140954
chr154297141042971764E07141094
chr154288296142883026E072-47290
chr154288318542883239E072-47077
chr154288334242883408E072-46908
chr154288354142883634E072-46682
chr154288368442884064E072-46252
chr154288414142884191E072-46125
chr154288712042887170E072-43146
chr154288756642887719E072-42597
chr154288773642888439E072-41877
chr154288866742888774E072-41542
chr154288880842888876E072-41440
chr154289717542898656E072-31660
chr154289999142901034E072-29282
chr154290104342901266E072-29050
chr154290130542901577E072-28739
chr154294251742942993E07212201
chr154296431042964461E07233994
chr154296478842964838E07234472
chr154296980142969851E07239485
chr154297004242970317E07239726
chr154297053242970634E07240216
chr154297067042970996E07240354
chr154297120242971256E07240886
chr154297127042971405E07240954
chr154297141042971764E07241094
chr154289999142901034E073-29282
chr154290104342901266E073-29050
chr154296980142969851E07339485
chr154297004242970317E07339726
chr154297053242970634E07340216
chr154297067042970996E07340354
chr154297120242971256E07340886
chr154297127042971405E07340954
chr154288058742880819E074-49497
chr154288296142883026E074-47290
chr154288318542883239E074-47077
chr154288334242883408E074-46908
chr154288354142883634E074-46682
chr154288368442884064E074-46252
chr154288414142884191E074-46125
chr154288426342884384E074-45932
chr154288631742886417E074-43899
chr154288645042886677E074-43639
chr154288681342886867E074-43449
chr154288712042887170E074-43146
chr154288756642887719E074-42597
chr154288773642888439E074-41877
chr154288866742888774E074-41542
chr154288880842888876E074-41440
chr154288917442889242E074-41074
chr154289717542898656E074-31660
chr154289999142901034E074-29282
chr154290104342901266E074-29050
chr154290130542901577E074-28739
chr154290378842904044E074-26272
chr154294228842942411E07411972
chr154294251742942993E07412201
chr154296359042963964E07433274
chr154296406642964177E07433750
chr154296431042964461E07433994
chr154296478842964838E07434472
chr154296980142969851E07439485
chr154297004242970317E07439726
chr154297053242970634E07440216
chr154297067042970996E07440354
chr154297120242971256E07440886
chr154297127042971405E07440954
chr154297141042971764E07441094
chr154288773642888439E081-41877