rs2999090

Homo sapiens
G>A
EEFSEC : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0113 (3388/29940,GnomAD)
G==0109 (3176/29118,TOPMED)
G==0104 (523/5008,1000G)
G==0117 (449/3854,ALSPAC)
G==0120 (444/3708,TWINSUK)
chr3:128212497 (GRCh38.p7) (3q21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.128212497G>A
GRCh37.p13 chr 3NC_000003.11:g.127931340G>A

Gene: EEFSEC, eukaryotic elongation factor, selenocysteine-tRNA-specific(plus strand)

Molecule type Change Amino acid[Codon] SO Term
EEFSEC transcriptNM_021937.4:c.N/AIntron Variant
EEFSEC transcript variant X4XM_005247696.2:c.N/AIntron Variant
EEFSEC transcript variant X1XM_017006975.1:c.N/AIntron Variant
EEFSEC transcript variant X2XM_017006976.1:c.N/AIntron Variant
EEFSEC transcript variant X3XM_017006977.1:c.N/AIntron Variant
EEFSEC transcript variant X5XM_017006978.1:c.N/AIntron Variant
EEFSEC transcript variant X7XM_017006980.1:c.N/AIntron Variant
EEFSEC transcript variant X7XM_011513066.2:c.N/AGenic Upstream Transcript Variant
EEFSEC transcript variant X6XM_017006979.1:c.N/AGenic Upstream Transcript Variant
EEFSEC transcript variant X9XM_017006981.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.123A=0.877
1000GenomesAmericanSub694G=0.120A=0.880
1000GenomesEast AsianSub1008G=0.007A=0.993
1000GenomesEuropeSub1006G=0.111A=0.889
1000GenomesGlobalStudy-wide5008G=0.104A=0.896
1000GenomesSouth AsianSub978G=0.170A=0.830
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.117A=0.883
The Genome Aggregation DatabaseAfricanSub8714G=0.112A=0.888
The Genome Aggregation DatabaseAmericanSub838G=0.120A=0.880
The Genome Aggregation DatabaseEast AsianSub1622G=0.002A=0.998
The Genome Aggregation DatabaseEuropeSub18464G=0.122A=0.877
The Genome Aggregation DatabaseGlobalStudy-wide29940G=0.113A=0.886
The Genome Aggregation DatabaseOtherSub302G=0.120A=0.880
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.109A=0.890
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.120A=0.880
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs29990900.000388alcohol dependence21314694

eQTL of rs2999090 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 rs2999090 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 )
chr3127886829127886916E067-44424
chr3127886968127887315E067-44025
chr3127898056127898269E067-33071
chr3127898473127898534E067-32806
chr3127913326127913421E067-17919
chr3127913805127913926E067-17414
chr3127914124127914216E067-17124
chr3127914318127914519E067-16821
chr3127914631127914762E067-16578
chr3127914766127914925E067-16415
chr3127917339127917525E067-13815
chr3127945773127946177E06714433
chr3127955523127955688E06724183
chr3127955771127955899E06724431
chr3127956415127957340E06725075
chr3127886829127886916E068-44424
chr3127886968127887315E068-44025
chr3127892776127893021E068-38319
chr3127893449127893504E068-37836
chr3127893692127893743E068-37597
chr3127893860127894011E068-37329
chr3127894118127894166E068-37174
chr3127894174127894224E068-37116
chr3127894251127894383E068-36957
chr3127899196127899348E068-31992
chr3127899399127899513E068-31827
chr3127900145127900262E068-31078
chr3127900280127900349E068-30991
chr3127913326127913421E068-17919
chr3127913805127913926E068-17414
chr3127914124127914216E068-17124
chr3127914318127914519E068-16821
chr3127914631127914762E068-16578
chr3127914766127914925E068-16415
chr3127917339127917525E068-13815
chr3127948342127948528E06817002
chr3127948571127948632E06817231
chr3127955182127955250E06823842
chr3127955523127955688E06824183
chr3127955771127955899E06824431
chr3127956415127957340E06825075
chr3127900145127900262E069-31078
chr3127900280127900349E069-30991
chr3127913805127913926E069-17414
chr3127914124127914216E069-17124
chr3127914318127914519E069-16821
chr3127914631127914762E069-16578
chr3127914766127914925E069-16415
chr3127917339127917525E069-13815
chr3127929385127929835E069-1505
chr3127945567127945763E06914227
chr3127945773127946177E06914433
chr3127948041127948181E06916701
chr3127948342127948528E06917002
chr3127950233127950297E06918893
chr3127955523127955688E06924183
chr3127955771127955899E06924431
chr3127956415127957340E06925075
chr3127957538127957712E06926198
chr3127958234127958416E06926894
chr3127913805127913926E070-17414
chr3127914124127914216E070-17124
chr3127914318127914519E070-16821
chr3127914631127914762E070-16578
chr3127914766127914925E070-16415
chr3127945567127945763E07014227
chr3127945773127946177E07014433
chr3127946756127946819E07015416
chr3127948041127948181E07016701
chr3127955523127955688E07024183
chr3127955771127955899E07024431
chr3127956415127957340E07025075
chr3127957538127957712E07026198
chr3127886829127886916E071-44424
chr3127886968127887315E071-44025
chr3127892776127893021E071-38319
chr3127893449127893504E071-37836
chr3127893692127893743E071-37597
chr3127893860127894011E071-37329
chr3127894118127894166E071-37174
chr3127894174127894224E071-37116
chr3127899399127899513E071-31827
chr3127900145127900262E071-31078
chr3127900280127900349E071-30991
chr3127913326127913421E071-17919
chr3127913805127913926E071-17414
chr3127914124127914216E071-17124
chr3127914318127914519E071-16821
chr3127914631127914762E071-16578
chr3127914766127914925E071-16415
chr3127915557127915774E071-15566
chr3127917339127917525E071-13815
chr3127929385127929835E071-1505
chr3127945773127946177E07114433
chr3127947779127947851E07116439
chr3127947855127947935E07116515
chr3127948041127948181E07116701
chr3127948342127948528E07117002
chr3127948571127948632E07117231
chr3127950405127950455E07119065
chr3127951701127951751E07120361
chr3127955523127955688E07124183
chr3127955771127955899E07124431
chr3127956415127957340E07125075
chr3127957538127957712E07126198
chr3127974221127974282E07142881
chr3127900145127900262E072-31078
chr3127900280127900349E072-30991
chr3127913326127913421E072-17919
chr3127913805127913926E072-17414
chr3127914124127914216E072-17124
chr3127914318127914519E072-16821
chr3127914631127914762E072-16578
chr3127914766127914925E072-16415
chr3127917339127917525E072-13815
chr3127929385127929835E072-1505
chr3127945023127945461E07213683
chr3127945567127945763E07214227
chr3127945773127946177E07214433
chr3127955523127955688E07224183
chr3127955771127955899E07224431
chr3127956415127957340E07225075
chr3127957538127957712E07226198
chr3127914124127914216E073-17124
chr3127914318127914519E073-16821
chr3127914631127914762E073-16578
chr3127914766127914925E073-16415
chr3127915557127915774E073-15566
chr3127948041127948181E07316701
chr3127948342127948528E07317002
chr3127956415127957340E07325075
chr3127974221127974282E07342881
chr3127974393127974573E07343053
chr3127886829127886916E074-44424
chr3127886968127887315E074-44025
chr3127893449127893504E074-37836
chr3127893692127893743E074-37597
chr3127893860127894011E074-37329
chr3127894118127894166E074-37174
chr3127894174127894224E074-37116
chr3127894251127894383E074-36957
chr3127898056127898269E074-33071
chr3127898473127898534E074-32806
chr3127899196127899348E074-31992
chr3127899399127899513E074-31827
chr3127900145127900262E074-31078
chr3127900280127900349E074-30991
chr3127912154127912302E074-19038
chr3127913326127913421E074-17919
chr3127913805127913926E074-17414
chr3127914124127914216E074-17124
chr3127914318127914519E074-16821
chr3127914631127914762E074-16578
chr3127914766127914925E074-16415
chr3127915557127915774E074-15566
chr3127929385127929835E074-1505
chr3127945773127946177E07414433
chr3127946756127946819E07415416
chr3127947779127947851E07416439
chr3127947855127947935E07416515
chr3127948041127948181E07416701
chr3127948342127948528E07417002
chr3127948571127948632E07417231
chr3127951701127951751E07420361
chr3127955523127955688E07424183
chr3127955771127955899E07424431
chr3127956415127957340E07425075
chr3127957538127957712E07426198
chr3127945023127945461E08113683
chr3127945567127945763E08114227
chr3127945773127946177E08114433
chr3127947779127947851E08116439
chr3127947855127947935E08116515
chr3127948041127948181E08116701
chr3127948342127948528E08117002
chr3127955182127955250E08123842
chr3127955523127955688E08124183
chr3127955771127955899E08124431
chr3127956415127957340E08125075
chr3127955182127955250E08223842
chr3127955523127955688E08224183
chr3127955771127955899E08224431
chr3127956415127957340E08225075