rs4608970

Homo sapiens
T>C
LPCAT1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0047 (1416/29996,GnomAD)
C=0056 (1633/29118,TOPMED)
C=0052 (261/5008,1000G)
C=0060 (232/3854,ALSPAC)
C=0067 (247/3708,TWINSUK)
chr5:1519082 (GRCh38.p7) (5p15.33)
AD
GWASdb2
1   publication(s)
See rs on genome
200 Enhancers around
38 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.1519082T>C
GRCh37.p13 chr 5NC_000005.9:g.1519197T>C

Gene: LPCAT1, lysophosphatidylcholine acyltransferase 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LPCAT1 transcriptNM_024830.3:c.N/AIntron Variant
LPCAT1 transcript variant X3XM_005248373.3:c.N/AIntron Variant
LPCAT1 transcript variant X1XM_011514132.1:c.N/AGenic Upstream Transcript Variant
LPCAT1 transcript variant X2XM_011514134.1:c.N/AGenic Upstream Transcript Variant
LPCAT1 transcript variant X4XM_017009879.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.946C=0.054
1000GenomesAmericanSub694T=0.940C=0.060
1000GenomesEast AsianSub1008T=1.000C=0.000
1000GenomesEuropeSub1006T=0.931C=0.069
1000GenomesGlobalStudy-wide5008T=0.948C=0.052
1000GenomesSouth AsianSub978T=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.940C=0.060
The Genome Aggregation DatabaseAfricanSub8732T=0.946C=0.054
The Genome Aggregation DatabaseAmericanSub838T=0.950C=0.050
The Genome Aggregation DatabaseEast AsianSub1620T=0.999C=0.001
The Genome Aggregation DatabaseEuropeSub18504T=0.953C=0.046
The Genome Aggregation DatabaseGlobalStudy-wide29996T=0.952C=0.047
The Genome Aggregation DatabaseOtherSub302T=0.880C=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.943C=0.056
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.933C=0.067
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
rs46089700.000023alcohol dependence20201924
rs46089700.0000235alcoholismpha002893
rs46089700.0000848alcoholismpha002892
rs46089700.000085alcohol dependenc(early age of onset)e20201924

eQTL of rs4608970 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 rs4608970 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 )
chr514974061497765E067-21432
chr514979251498556E067-20641
chr515058031505931E067-13266
chr515059621506194E067-13003
chr515061991506361E067-12836
chr515217511521931E0672554
chr515220221522072E0672825
chr515535211553583E06734324
chr514974061497765E068-21432
chr514979251498556E068-20641
chr514986071498981E068-20216
chr515011531501216E068-17981
chr515044041504566E068-14631
chr515055681505634E068-13563
chr515058031505931E068-13266
chr515059621506194E068-13003
chr515061991506361E068-12836
chr515065441506905E068-12292
chr515070861507152E068-12045
chr515220221522072E0682825
chr515249501525027E0685753
chr515518111552414E06832614
chr515535211553583E06834324
chr515537401553805E06834543
chr514974061497765E069-21432
chr514979251498556E069-20641
chr514986071498981E069-20216
chr515058031505931E069-13266
chr515065441506905E069-12292
chr515070861507152E069-12045
chr515216391521708E0692442
chr515217511521931E0692554
chr515249501525027E0695753
chr515526041553389E06933407
chr515535211553583E06934324
chr515537401553805E06934543
chr514974061497765E070-21432
chr514979251498556E070-20641
chr514986071498981E070-20216
chr515000251500108E070-19089
chr515001311500207E070-18990
chr515004011500529E070-18668
chr515005951500862E070-18335
chr515011531501216E070-17981
chr515014851501590E070-17607
chr515033181504290E070-14907
chr515055681505634E070-13563
chr515058031505931E070-13266
chr515059621506194E070-13003
chr515061991506361E070-12836
chr515065441506905E070-12292
chr515070861507152E070-12045
chr515077491507897E070-11300
chr515087391508807E070-10390
chr515144801515267E070-3930
chr515154021515806E070-3391
chr515249501525027E0705753
chr515250511525121E0705854
chr515537401553805E07034543
chr515539131553993E07034716
chr515541461554214E07034949
chr514974061497765E071-21432
chr515000251500108E071-19089
chr515005951500862E071-18335
chr515011531501216E071-17981
chr515055681505634E071-13563
chr515058031505931E071-13266
chr515059621506194E071-13003
chr515061991506361E071-12836
chr515065441506905E071-12292
chr515070861507152E071-12045
chr515220221522072E0712825
chr515418191542570E07122622
chr515442271544358E07125030
chr515535211553583E07134324
chr515537401553805E07134543
chr515539131553993E07134716
chr515682011568278E07149004
chr515682861569068E07149089
chr514795971480218E072-38979
chr514974061497765E072-21432
chr514979251498556E072-20641
chr514986071498981E072-20216
chr515055681505634E072-13563
chr515058031505931E072-13266
chr515059621506194E072-13003
chr515061991506361E072-12836
chr515217511521931E0722554
chr515220221522072E0722825
chr515535211553583E07234324
chr514974061497765E073-21432
chr514979251498556E073-20641
chr514986071498981E073-20216
chr514989961499551E073-19646
chr515055681505634E073-13563
chr515058031505931E073-13266
chr515059621506194E073-13003
chr515061991506361E073-12836
chr515092891509339E073-9858
chr515161331517015E073-2182
chr515220221522072E0732825
chr515484271548571E07329230
chr515535211553583E07334324
chr515537401553805E07334543
chr515539131553993E07334716
chr515661181566193E07346921
chr515666041566664E07347407
chr515682011568278E07349004
chr515682861569068E07349089
chr514974061497765E074-21432
chr514979251498556E074-20641
chr514986071498981E074-20216
chr514989961499551E074-19646
chr515027571503276E074-15921
chr515033181504290E074-14907
chr515065441506905E074-12292
chr515070861507152E074-12045
chr515535211553583E07434324
chr515537401553805E07434543
chr514974061497765E081-21432
chr514979251498556E081-20641
chr514989961499551E081-19646
chr515000251500108E081-19089
chr515001311500207E081-18990
chr515004011500529E081-18668
chr515005951500862E081-18335
chr515011531501216E081-17981
chr515055681505634E081-13563
chr515058031505931E081-13266
chr515059621506194E081-13003
chr515061991506361E081-12836
chr515065441506905E081-12292
chr515070861507152E081-12045
chr515144801515267E081-3930
chr515154021515806E081-3391
chr515159071516042E081-3155
chr515217511521931E0812554
chr515220221522072E0812825
chr515249501525027E0815753
chr515409721541033E08121775
chr515414071541559E08122210
chr515418191542570E08122622
chr515429161543215E08123719
chr515450911545444E08125894
chr515455681545639E08126371
chr515458921546339E08126695
chr515464001546650E08127203
chr515467231546863E08127526
chr515471391547228E08127942
chr515484271548571E08129230
chr515503931550464E08131196
chr515518111552414E08132614
chr515526041553389E08133407
chr515535211553583E08134324
chr515537401553805E08134543
chr515539131553993E08134716
chr515541461554214E08134949
chr515548491554947E08135652
chr515550931555327E08135896
chr515554211555844E08136224
chr514974061497765E082-21432
chr514979251498556E082-20641
chr514986071498981E082-20216
chr514989961499551E082-19646
chr515005951500862E082-18335
chr515011531501216E082-17981
chr515055681505634E082-13563
chr515058031505931E082-13266
chr515059621506194E082-13003
chr515061991506361E082-12836
chr515065441506905E082-12292
chr515070861507152E082-12045
chr515077491507897E082-11300
chr515144801515267E082-3930
chr515154021515806E082-3391
chr515159071516042E082-3155
chr515161331517015E082-2182
chr515170271517579E082-1618
chr515210101521471E0821813
chr515216391521708E0822442
chr515217511521931E0822554
chr515249501525027E0825753
chr515250511525121E0825854
chr515401641540229E08220967
chr515403781540532E08221181
chr515407941540844E08221597
chr515409721541033E08221775
chr515414071541559E08222210
chr515418191542570E08222622
chr515455681545639E08226371
chr515456711545776E08226474
chr515494671549637E08230270
chr515503931550464E08231196
chr515535211553583E08234324
chr515537401553805E08234543
chr515539131553993E08234716
chr515541461554214E08234949
chr515548491554947E08235652
chr515550931555327E08235896
chr515554211555844E08236224










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr515229291523014E0673732
chr515230861523207E0673889
chr515232811523489E0674084
chr515235961524945E0674399
chr515229291523014E0683732
chr515230861523207E0683889
chr515232811523489E0684084
chr515235961524945E0684399
chr515229291523014E0693732
chr515230861523207E0693889
chr515232811523489E0694084
chr515235961524945E0694399
chr515229291523014E0703732
chr515230861523207E0703889
chr515232811523489E0704084
chr515235961524945E0704399
chr515229291523014E0713732
chr515230861523207E0713889
chr515232811523489E0714084
chr515235961524945E0714399
chr515229291523014E0723732
chr515230861523207E0723889
chr515232811523489E0724084
chr515235961524945E0724399
chr515229291523014E0733732
chr515230861523207E0733889
chr515232811523489E0734084
chr515235961524945E0734399
chr515229291523014E0743732
chr515230861523207E0743889
chr515232811523489E0744084
chr515235961524945E0744399
chr515229291523014E0813732
chr515230861523207E0813889
chr515229291523014E0823732
chr515230861523207E0823889
chr515232811523489E0824084
chr515235961524945E0824399