rs4790689

Homo sapiens
A>C
PELP1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0340 (10192/29916,GnomAD)
A==0404 (11783/29118,TOPMED)
A==0305 (1527/5008,1000G)
A==0289 (1114/3854,ALSPAC)
A==0305 (1132/3708,TWINSUK)
chr17:4701905 (GRCh38.p7) (17p13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
32 Enhancers around
43 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.4701905A>C
GRCh37.p13 chr 17NC_000017.10:g.4605200A>C

Gene: PELP1, proline, glutamate and leucine rich protein 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PELP1 transcript variant 2NM_001278241.1:c.N/AIntron Variant
PELP1 transcript variant 1NM_014389.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.517C=0.483
1000GenomesAmericanSub694A=0.280C=0.720
1000GenomesEast AsianSub1008A=0.169C=0.831
1000GenomesEuropeSub1006A=0.304C=0.696
1000GenomesGlobalStudy-wide5008A=0.305C=0.695
1000GenomesSouth AsianSub978A=0.180C=0.820
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.289C=0.711
The Genome Aggregation DatabaseAfricanSub8708A=0.498C=0.502
The Genome Aggregation DatabaseAmericanSub838A=0.250C=0.750
The Genome Aggregation DatabaseEast AsianSub1618A=0.200C=0.800
The Genome Aggregation DatabaseEuropeSub18450A=0.283C=0.716
The Genome Aggregation DatabaseGlobalStudy-wide29916A=0.340C=0.659
The Genome Aggregation DatabaseOtherSub302A=0.310C=0.690
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.404C=0.595
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.305C=0.695
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
rs47906890.000427alcohol dependence20201924

eQTL of rs4790689 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr17:4605200ALOX15ENSG00000161905.8A>C3.7844e-959611Cerebellum
Chr17:4605200ALOX15ENSG00000161905.8A>C9.8439e-759611Hypothalamus
Chr17:4605200ALOX15ENSG00000161905.8A>C7.5914e-1059611Cortex
Chr17:4605200ALOX15ENSG00000161905.8A>C1.3738e-859611Anterior_cingulate_cortex

meQTL of rs4790689 in Fetal Brain

Probe ID Position Gene beta p-value
cg24831541chr17:4613045ARRB2-0.04079010250539385.7938e-9

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 )
chr1746059934606164E067793
chr1746082854608402E0683085
chr1746359094636292E06830709
chr1746363644636551E06831164
chr1745944044594444E069-10756
chr1745945494594602E069-10598
chr1746057114605824E069511
chr1746058384605906E069638
chr1746059934606164E069793
chr1746048844604940E070-260
chr1746049744605024E070-176
chr1746050374605148E070-52
chr1746052594605327E07059
chr1746057114605824E070511
chr1746058384605906E070638
chr1746059934606164E070793
chr1746050374605148E071-52
chr1746057114605824E071511
chr1746058384605906E071638
chr1746059934606164E071793
chr1746190994619198E07113899
chr1746439234643973E07138723
chr1746059934606164E072793
chr1746082854608402E0723085
chr1746082854608402E0733085
chr1746356944635744E07430494
chr1746359094636292E07430709
chr1745710024571411E081-33789
chr1746059934606164E081793
chr1746082854608402E0813085
chr1746057114605824E082511
chr1746058384605906E082638










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1746067034607788E0671503
chr1746078194607923E0672619
chr1746336904635395E06728490
chr1746414924643765E06736292
chr1746067034607788E0681503
chr1746078194607923E0682619
chr1746336904635395E06828490
chr1746414924643765E06836292
chr1746067034607788E0691503
chr1746078194607923E0692619
chr1746080624608164E0692862
chr1746336904635395E06928490
chr1746414924643765E06936292
chr1746067034607788E0701503
chr1746078194607923E0702619
chr1746080624608164E0702862
chr1746336904635395E07028490
chr1746067034607788E0711503
chr1746078194607923E0712619
chr1746080624608164E0712862
chr1746336904635395E07128490
chr1746414924643765E07136292
chr1746067034607788E0721503
chr1746078194607923E0722619
chr1746080624608164E0722862
chr1746336904635395E07228490
chr1746414924643765E07236292
chr1746067034607788E0731503
chr1746078194607923E0732619
chr1746080624608164E0732862
chr1746336904635395E07328490
chr1746414924643765E07336292
chr1746067034607788E0741503
chr1746078194607923E0742619
chr1746336904635395E07428490
chr1746414924643765E07436292
chr1746483894649039E07443189
chr1746067034607788E0811503
chr1746336904635395E08128490
chr1746067034607788E0821503
chr1746078194607923E0822619
chr1746080624608164E0822862
chr1746336904635395E08228490