rs9654453

Homo sapiens
T>C
PDCD6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0110 (3280/29716,GnomAD)
C=0144 (4201/29118,TOPMED)
C=0110 (549/5008,1000G)
C=0130 (502/3854,ALSPAC)
C=0128 (475/3708,TWINSUK)
chr5:299506 (GRCh38.p7) (5p15.33)
AD
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
78 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.299506T>C
GRCh37.p13 chr 5NC_000005.9:g.299621T>C
AHRR RefSeqGeneNG_029834.1:g.331T>C

Gene: PDCD6, programmed cell death 6(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PDCD6 transcript variant 2NM_001267556.1:c.N/AIntron Variant
PDCD6 transcript variant 3NM_001267557.1:c.N/AIntron Variant
PDCD6 transcript variant 4NM_001267558.1:c.N/AIntron Variant
PDCD6 transcript variant 5NM_001267559.1:c.N/AIntron Variant
PDCD6 transcript variant 1NM_013232.3:c.N/AIntron Variant
PDCD6 transcript variant 6NR_073609.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.866C=0.134
1000GenomesAmericanSub694T=0.810C=0.190
1000GenomesEast AsianSub1008T=0.941C=0.059
1000GenomesEuropeSub1006T=0.896C=0.104
1000GenomesGlobalStudy-wide5008T=0.890C=0.110
1000GenomesSouth AsianSub978T=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.870C=0.130
The Genome Aggregation DatabaseAfricanSub8670T=0.871C=0.129
The Genome Aggregation DatabaseAmericanSub834T=0.850C=0.150
The Genome Aggregation DatabaseEast AsianSub1622T=0.950C=0.050
The Genome Aggregation DatabaseEuropeSub18288T=0.895C=0.104
The Genome Aggregation DatabaseGlobalStudy-wide29716T=0.889C=0.110
The Genome Aggregation DatabaseOtherSub302T=0.840C=0.160
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.855C=0.144
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.872C=0.128
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
rs96544530.00096alcohol dependence20201924

eQTL of rs9654453 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr5:299621AHRRENSG00000063438.12T>C7.6099e-4-4670Frontal_Cortex_BA9
Chr5:299621AHRRENSG00000063438.12T>C1.5183e-5-4670Cortex

meQTL of rs9654453 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 )
chr5317147317733E06717526
chr5317147317733E06917526
chr5310763310890E07111142
chr5290862290912E073-8709
chr5310432310623E07310811
chr5310763310890E07311142
chr5319479319552E07319858
chr5345184345238E08145563
chr5345645345922E08146024





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5271138272029E067-27592
chr5272071272126E067-27495
chr5272348272390E067-27231
chr5272536272586E067-27035
chr5321295321936E06721674
chr5321937322102E06722316
chr5322113322223E06722492
chr5322347322437E06722726
chr5322524322897E06722903
chr5343964344547E06744343
chr5270961271092E068-28529
chr5271138272029E068-27592
chr5272071272126E068-27495
chr5272348272390E068-27231
chr5272536272586E068-27035
chr5321937322102E06822316
chr5322113322223E06822492
chr5322347322437E06822726
chr5343964344547E06844343
chr5270961271092E069-28529
chr5271138272029E069-27592
chr5272071272126E069-27495
chr5272348272390E069-27231
chr5272536272586E069-27035
chr5320717321033E06921096
chr5321937322102E06922316
chr5322113322223E06922492
chr5343964344547E06944343
chr5270961271092E070-28529
chr5271138272029E070-27592
chr5272071272126E070-27495
chr5321937322102E07022316
chr5343677343932E07044056
chr5343964344547E07044343
chr5270961271092E071-28529
chr5271138272029E071-27592
chr5272071272126E071-27495
chr5272348272390E071-27231
chr5272536272586E071-27035
chr5321937322102E07122316
chr5322113322223E07122492
chr5322347322437E07122726
chr5322524322897E07122903
chr5343964344547E07144343
chr5270961271092E072-28529
chr5271138272029E072-27592
chr5272071272126E072-27495
chr5272348272390E072-27231
chr5272536272586E072-27035
chr5320717321033E07221096
chr5321295321936E07221674
chr5321937322102E07222316
chr5322113322223E07222492
chr5322347322437E07222726
chr5343964344547E07244343
chr5270961271092E073-28529
chr5271138272029E073-27592
chr5321295321936E07321674
chr5321937322102E07322316
chr5322113322223E07322492
chr5322347322437E07322726
chr5322524322897E07322903
chr5343964344547E07344343
chr5270961271092E074-28529
chr5271138272029E074-27592
chr5321295321936E07421674
chr5343964344547E07444343
chr5270961271092E082-28529
chr5271138272029E082-27592
chr5272071272126E082-27495
chr5272348272390E082-27231
chr5272536272586E082-27035
chr5321295321936E08221674
chr5321937322102E08222316
chr5322113322223E08222492
chr5322347322437E08222726
chr5343677343932E08244056
chr5343964344547E08244343