rs2028201

Homo sapiens
G>T
SPATS2L : Intron Variant
LOC101927741 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0329 (9810/29822,GnomAD)
T=0300 (8762/29118,TOPMED)
T=0327 (1640/5008,1000G)
T=0396 (1526/3854,ALSPAC)
T=0388 (1437/3708,TWINSUK)
chr2:200438287 (GRCh38.p7) (2q33.1)
AD
GWASCatalog
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.200438287G>T
GRCh37.p13 chr 2NC_000002.11:g.201303010G>T

Gene: SPATS2L, spermatogenesis associated serine rich 2 like(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SPATS2L transcript variant 2NM_001100422.1:c.N/AIntron Variant
SPATS2L transcript variant 3NM_001100423.1:c.N/AIntron Variant
SPATS2L transcript variant 4NM_001100424.1:c.N/AIntron Variant
SPATS2L transcript variant 5NM_001282735.1:c.N/AIntron Variant
SPATS2L transcript variant 6NM_001282743.1:c.N/AIntron Variant
SPATS2L transcript variant 7NM_001282744.1:c.N/AIntron Variant
SPATS2L transcript variant 1NM_015535.2:c.N/AIntron Variant
SPATS2L transcript variant X5XM_005246456.1:c.N/AIntron Variant
SPATS2L transcript variant X7XM_005246457.1:c.N/AIntron Variant
SPATS2L transcript variant X4XM_005246458.1:c.N/AIntron Variant
SPATS2L transcript variant X10XM_005246459.1:c.N/AIntron Variant
SPATS2L transcript variant X1XM_011510938.1:c.N/AIntron Variant
SPATS2L transcript variant X3XM_011510939.1:c.N/AIntron Variant
SPATS2L transcript variant X2XM_017003783.1:c.N/AIntron Variant
SPATS2L transcript variant X7XM_017003784.1:c.N/AIntron Variant
SPATS2L transcript variant X9XM_017003785.1:c.N/AIntron Variant
SPATS2L transcript variant X13XM_017003786.1:c.N/AIntron Variant
SPATS2L transcript variant X14XM_017003787.1:c.N/AIntron Variant

Gene: LOC101927741, uncharacterized LOC101927741(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC101927741 transcript variant X2XR_001739165.1:n.N/AIntron Variant
LOC101927741 transcript variant X3XR_001739166.1:n.N/AIntron Variant
LOC101927741 transcript variant X4XR_001739167.1:n.N/AIntron Variant
LOC101927741 transcript variant X1XR_001739164.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.836T=0.164
1000GenomesAmericanSub694G=0.690T=0.310
1000GenomesEast AsianSub1008G=0.598T=0.402
1000GenomesEuropeSub1006G=0.622T=0.378
1000GenomesGlobalStudy-wide5008G=0.673T=0.327
1000GenomesSouth AsianSub978G=0.570T=0.430
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.604T=0.396
The Genome Aggregation DatabaseAfricanSub8648G=0.804T=0.196
The Genome Aggregation DatabaseAmericanSub826G=0.690T=0.310
The Genome Aggregation DatabaseEast AsianSub1606G=0.570T=0.430
The Genome Aggregation DatabaseEuropeSub18442G=0.617T=0.382
The Genome Aggregation DatabaseGlobalStudy-wide29822G=0.671T=0.329
The Genome Aggregation DatabaseOtherSub300G=0.610T=0.390
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.699T=0.300
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.612T=0.388
PMID Title Author Journal
28714907Genetic Contribution to Alcohol Dependence: Investigation of a Heterogeneous German Sample of Individuals with Alcohol Dependence, Chronic Alcoholic Pancreatitis, and Alcohol-Related Cirrhosis.Treutlein JGenes (Basel)

P-Value

SNP ID p-value Traits Study
rs20282015E-06alcohol dependence28714907

eQTL of rs2028201 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 rs2028201 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 )
chr2201261417201261938E067-41072
chr2201261955201262047E067-40963
chr2201262464201262894E067-40116
chr2201270074201271500E067-31510
chr2201271759201271809E067-31201
chr2201273090201273630E067-29380
chr2201276649201276874E067-26136
chr2201307185201307695E0674175
chr2201307841201307955E0674831
chr2201308731201309011E0675721
chr2201309444201309496E0676434
chr2201309674201309727E0676664
chr2201310279201310329E0677269
chr2201318691201318762E06715681
chr2201318794201318927E06715784
chr2201319883201320148E06716873
chr2201320267201320490E06717257
chr2201320600201320654E06717590
chr2201320711201321204E06717701
chr2201321478201321551E06718468
chr2201322340201322483E06719330
chr2201332615201332662E06729605
chr2201332755201333059E06729745
chr2201333093201333239E06730083
chr2201333304201333593E06730294
chr2201333605201333645E06730595
chr2201333948201334140E06730938
chr2201334362201334847E06731352
chr2201334874201334950E06731864
chr2201262464201262894E068-40116
chr2201270074201271500E068-31510
chr2201271759201271809E068-31201
chr2201307185201307695E0684175
chr2201318691201318762E06815681
chr2201318794201318927E06815784
chr2201319011201319123E06816001
chr2201319883201320148E06816873
chr2201320267201320490E06817257
chr2201320600201320654E06817590
chr2201320711201321204E06817701
chr2201321478201321551E06818468
chr2201322340201322483E06819330
chr2201330226201330266E06827216
chr2201332615201332662E06829605
chr2201332755201333059E06829745
chr2201333093201333239E06830083
chr2201333304201333593E06830294
chr2201333605201333645E06830595
chr2201333948201334140E06830938
chr2201334362201334847E06831352
chr2201334874201334950E06831864
chr2201334999201335414E06831989
chr2201335595201335692E06832585
chr2201336063201336399E06833053
chr2201341337201341402E06838327
chr2201261417201261938E069-41072
chr2201261955201262047E069-40963
chr2201262464201262894E069-40116
chr2201270074201271500E069-31510
chr2201272890201273014E069-29996
chr2201273090201273630E069-29380
chr2201307185201307695E0694175
chr2201314086201314147E06911076
chr2201318691201318762E06915681
chr2201318794201318927E06915784
chr2201320267201320490E06917257
chr2201320600201320654E06917590
chr2201320711201321204E06917701
chr2201321478201321551E06918468
chr2201322340201322483E06919330
chr2201332615201332662E06929605
chr2201332755201333059E06929745
chr2201333093201333239E06930083
chr2201333304201333593E06930294
chr2201333605201333645E06930595
chr2201333948201334140E06930938
chr2201334362201334847E06931352
chr2201334999201335414E06931989
chr2201335595201335692E06932585
chr2201336063201336399E06933053
chr2201336838201337160E06933828
chr2201341337201341402E06938327
chr2201261417201261938E070-41072
chr2201261955201262047E070-40963
chr2201281701201281843E070-21167
chr2201282098201282178E070-20832
chr2201282285201282390E070-20620
chr2201318691201318762E07015681
chr2201320267201320490E07017257
chr2201320600201320654E07017590
chr2201320711201321204E07017701
chr2201321478201321551E07018468
chr2201328287201328459E07025277
chr2201334362201334847E07031352
chr2201334874201334950E07031864
chr2201334999201335414E07031989
chr2201262464201262894E071-40116
chr2201270074201271500E071-31510
chr2201272580201272630E071-30380
chr2201272672201272817E071-30193
chr2201272890201273014E071-29996
chr2201273090201273630E071-29380
chr2201276649201276874E071-26136
chr2201318691201318762E07115681
chr2201318794201318927E07115784
chr2201319011201319123E07116001
chr2201319883201320148E07116873
chr2201320267201320490E07117257
chr2201320600201320654E07117590
chr2201320711201321204E07117701
chr2201321478201321551E07118468
chr2201322340201322483E07119330
chr2201324284201324354E07121274
chr2201332615201332662E07129605
chr2201332755201333059E07129745
chr2201333093201333239E07130083
chr2201333304201333593E07130294
chr2201333605201333645E07130595
chr2201333948201334140E07130938
chr2201334362201334847E07131352
chr2201334999201335414E07131989
chr2201335595201335692E07132585
chr2201336063201336399E07133053
chr2201336838201337160E07133828
chr2201262464201262894E072-40116
chr2201270074201271500E072-31510
chr2201273090201273630E072-29380
chr2201276649201276874E072-26136
chr2201314086201314147E07211076
chr2201314560201314643E07211550
chr2201318691201318762E07215681
chr2201318794201318927E07215784
chr2201320267201320490E07217257
chr2201320600201320654E07217590
chr2201320711201321204E07217701
chr2201321478201321551E07218468
chr2201322340201322483E07219330
chr2201324284201324354E07221274
chr2201332615201332662E07229605
chr2201332755201333059E07229745
chr2201333093201333239E07230083
chr2201333304201333593E07230294
chr2201333605201333645E07230595
chr2201333948201334140E07230938
chr2201335595201335692E07232585
chr2201336063201336399E07233053
chr2201261955201262047E073-40963
chr2201262464201262894E073-40116
chr2201270074201271500E073-31510
chr2201272890201273014E073-29996
chr2201320267201320490E07317257
chr2201320600201320654E07317590
chr2201320711201321204E07317701
chr2201321478201321551E07318468
chr2201322340201322483E07319330
chr2201332615201332662E07329605
chr2201332755201333059E07329745
chr2201333093201333239E07330083
chr2201334999201335414E07331989
chr2201335595201335692E07332585
chr2201261417201261938E074-41072
chr2201261955201262047E074-40963
chr2201262464201262894E074-40116
chr2201270074201271500E074-31510
chr2201271759201271809E074-31201
chr2201307185201307695E0744175
chr2201307841201307955E0744831
chr2201308731201309011E0745721
chr2201309444201309496E0746434
chr2201309674201309727E0746664
chr2201318691201318762E07415681
chr2201318794201318927E07415784
chr2201320267201320490E07417257
chr2201320600201320654E07417590
chr2201320711201321204E07417701
chr2201321478201321551E07418468
chr2201322340201322483E07419330
chr2201324284201324354E07421274
chr2201330226201330266E07427216
chr2201332615201332662E07429605
chr2201332755201333059E07429745
chr2201333093201333239E07430083
chr2201333304201333593E07430294
chr2201333605201333645E07430595
chr2201333948201334140E07430938
chr2201334362201334847E07431352
chr2201334874201334950E07431864
chr2201334999201335414E07431989
chr2201335595201335692E07432585
chr2201336063201336399E07433053
chr2201336838201337160E07433828
chr2201261417201261938E081-41072
chr2201261955201262047E081-40963
chr2201262464201262894E081-40116
chr2201334362201334847E08131352
chr2201334874201334950E08131864
chr2201261955201262047E082-40963
chr2201262464201262894E082-40116
chr2201303549201303953E082539
chr2201304004201304150E082994










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2201341676201341814E06738666
chr2201341955201342005E06738945
chr2201341676201341814E06838666
chr2201341955201342005E06838945
chr2201341676201341814E06938666
chr2201341955201342005E06938945
chr2201342362201342467E06939352
chr2201342527201342611E06939517
chr2201341676201341814E07138666
chr2201341955201342005E07138945
chr2201342362201342467E07139352
chr2201342527201342611E07139517
chr2201341676201341814E07238666
chr2201341955201342005E07238945
chr2201342362201342467E07239352
chr2201342527201342611E07239517
chr2201341676201341814E07438666
chr2201341955201342005E07438945
chr2201342362201342467E07439352
chr2201342527201342611E07439517