rs4790687

Homo sapiens
A>G
PELP1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0339 (10067/29626,GnomAD)
A==0404 (11780/29118,TOPMED)
A==0305 (1528/5008,1000G)
A==0287 (1108/3854,ALSPAC)
A==0300 (1112/3708,TWINSUK)
chr17:4701339 (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.4701339A>G
GRCh37.p13 chr 17NC_000017.10:g.4604634A>G

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=0.517G=0.483
1000GenomesAmericanSub694A=0.280G=0.720
1000GenomesEast AsianSub1008A=0.170G=0.830
1000GenomesEuropeSub1006A=0.303G=0.697
1000GenomesGlobalStudy-wide5008A=0.305G=0.695
1000GenomesSouth AsianSub978A=0.180G=0.820
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.287G=0.713
The Genome Aggregation DatabaseAfricanSub8588A=0.496G=0.504
The Genome Aggregation DatabaseAmericanSub832A=0.250G=0.750
The Genome Aggregation DatabaseEast AsianSub1574A=0.194G=0.806
The Genome Aggregation DatabaseEuropeSub18334A=0.283G=0.716
The Genome Aggregation DatabaseGlobalStudy-wide29626A=0.339G=0.660
The Genome Aggregation DatabaseOtherSub298A=0.310G=0.690
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.404G=0.595
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.300G=0.700
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
rs47906870.000431alcohol dependence20201924

eQTL of rs4790687 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr17:4604634ALOX15ENSG00000161905.8A>G3.7844e-959045Cerebellum
Chr17:4604634ALOX15ENSG00000161905.8A>G9.8439e-759045Hypothalamus
Chr17:4604634ALOX15ENSG00000161905.8A>G7.5914e-1059045Cortex
Chr17:4604634ALOX15ENSG00000161905.8A>G1.3738e-859045Anterior_cingulate_cortex

meQTL of rs4790687 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 )
chr1746059934606164E0671359
chr1746082854608402E0683651
chr1746359094636292E06831275
chr1746363644636551E06831730
chr1745944044594444E069-10190
chr1745945494594602E069-10032
chr1746057114605824E0691077
chr1746058384605906E0691204
chr1746059934606164E0691359
chr1746048844604940E070250
chr1746049744605024E070340
chr1746050374605148E070403
chr1746052594605327E070625
chr1746057114605824E0701077
chr1746058384605906E0701204
chr1746059934606164E0701359
chr1746050374605148E071403
chr1746057114605824E0711077
chr1746058384605906E0711204
chr1746059934606164E0711359
chr1746190994619198E07114465
chr1746439234643973E07139289
chr1746059934606164E0721359
chr1746082854608402E0723651
chr1746082854608402E0733651
chr1746356944635744E07431060
chr1746359094636292E07431275
chr1745710024571411E081-33223
chr1746059934606164E0811359
chr1746082854608402E0813651
chr1746057114605824E0821077
chr1746058384605906E0821204










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1746067034607788E0672069
chr1746078194607923E0673185
chr1746336904635395E06729056
chr1746414924643765E06736858
chr1746067034607788E0682069
chr1746078194607923E0683185
chr1746336904635395E06829056
chr1746414924643765E06836858
chr1746067034607788E0692069
chr1746078194607923E0693185
chr1746080624608164E0693428
chr1746336904635395E06929056
chr1746414924643765E06936858
chr1746067034607788E0702069
chr1746078194607923E0703185
chr1746080624608164E0703428
chr1746336904635395E07029056
chr1746067034607788E0712069
chr1746078194607923E0713185
chr1746080624608164E0713428
chr1746336904635395E07129056
chr1746414924643765E07136858
chr1746067034607788E0722069
chr1746078194607923E0723185
chr1746080624608164E0723428
chr1746336904635395E07229056
chr1746414924643765E07236858
chr1746067034607788E0732069
chr1746078194607923E0733185
chr1746080624608164E0733428
chr1746336904635395E07329056
chr1746414924643765E07336858
chr1746067034607788E0742069
chr1746078194607923E0743185
chr1746336904635395E07429056
chr1746414924643765E07436858
chr1746483894649039E07443755
chr1746067034607788E0812069
chr1746336904635395E08129056
chr1746067034607788E0822069
chr1746078194607923E0823185
chr1746080624608164E0823428
chr1746336904635395E08229056