rs4790688

Homo sapiens
C>T
PELP1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0339 (10160/29934,GnomAD)
C==0404 (11779/29118,TOPMED)
C==0305 (1527/5008,1000G)
C==0289 (1112/3854,ALSPAC)
C==0304 (1126/3708,TWINSUK)
chr17:4701773 (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.4701773C>T
GRCh37.p13 chr 17NC_000017.10:g.4605068C>T

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
1000GenomesAfricanSub1322C=0.517T=0.483
1000GenomesAmericanSub694C=0.280T=0.720
1000GenomesEast AsianSub1008C=0.170T=0.830
1000GenomesEuropeSub1006C=0.303T=0.697
1000GenomesGlobalStudy-wide5008C=0.305T=0.695
1000GenomesSouth AsianSub978C=0.180T=0.820
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.289T=0.711
The Genome Aggregation DatabaseAfricanSub8702C=0.496T=0.504
The Genome Aggregation DatabaseAmericanSub838C=0.250T=0.750
The Genome Aggregation DatabaseEast AsianSub1614C=0.197T=0.803
The Genome Aggregation DatabaseEuropeSub18478C=0.282T=0.717
The Genome Aggregation DatabaseGlobalStudy-wide29934C=0.339T=0.660
The Genome Aggregation DatabaseOtherSub302C=0.310T=0.690
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.404T=0.595
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.304T=0.696
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
rs47906880.000427alcohol dependence20201924

eQTL of rs4790688 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr17:4605068ALOX15ENSG00000161905.8C>T3.7844e-959479Cerebellum
Chr17:4605068ALOX15ENSG00000161905.8C>T9.8439e-759479Hypothalamus
Chr17:4605068ALOX15ENSG00000161905.8C>T7.5914e-1059479Cortex
Chr17:4605068ALOX15ENSG00000161905.8C>T1.3738e-859479Anterior_cingulate_cortex

meQTL of rs4790688 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 )
chr1746059934606164E067925
chr1746082854608402E0683217
chr1746359094636292E06830841
chr1746363644636551E06831296
chr1745944044594444E069-10624
chr1745945494594602E069-10466
chr1746057114605824E069643
chr1746058384605906E069770
chr1746059934606164E069925
chr1746048844604940E070-128
chr1746049744605024E070-44
chr1746050374605148E0700
chr1746052594605327E070191
chr1746057114605824E070643
chr1746058384605906E070770
chr1746059934606164E070925
chr1746050374605148E0710
chr1746057114605824E071643
chr1746058384605906E071770
chr1746059934606164E071925
chr1746190994619198E07114031
chr1746439234643973E07138855
chr1746059934606164E072925
chr1746082854608402E0723217
chr1746082854608402E0733217
chr1746356944635744E07430626
chr1746359094636292E07430841
chr1745710024571411E081-33657
chr1746059934606164E081925
chr1746082854608402E0813217
chr1746057114605824E082643
chr1746058384605906E082770










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1746067034607788E0671635
chr1746078194607923E0672751
chr1746336904635395E06728622
chr1746414924643765E06736424
chr1746067034607788E0681635
chr1746078194607923E0682751
chr1746336904635395E06828622
chr1746414924643765E06836424
chr1746067034607788E0691635
chr1746078194607923E0692751
chr1746080624608164E0692994
chr1746336904635395E06928622
chr1746414924643765E06936424
chr1746067034607788E0701635
chr1746078194607923E0702751
chr1746080624608164E0702994
chr1746336904635395E07028622
chr1746067034607788E0711635
chr1746078194607923E0712751
chr1746080624608164E0712994
chr1746336904635395E07128622
chr1746414924643765E07136424
chr1746067034607788E0721635
chr1746078194607923E0722751
chr1746080624608164E0722994
chr1746336904635395E07228622
chr1746414924643765E07236424
chr1746067034607788E0731635
chr1746078194607923E0732751
chr1746080624608164E0732994
chr1746336904635395E07328622
chr1746414924643765E07336424
chr1746067034607788E0741635
chr1746078194607923E0742751
chr1746336904635395E07428622
chr1746414924643765E07436424
chr1746483894649039E07443321
chr1746067034607788E0811635
chr1746336904635395E08128622
chr1746067034607788E0821635
chr1746078194607923E0822751
chr1746080624608164E0822994
chr1746336904635395E08228622