rs2743189

Homo sapiens
C>T
PAX7 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0276 (8266/29862,GnomAD)
T=0299 (8729/29118,TOPMED)
T=0261 (1309/5008,1000G)
T=0220 (848/3854,ALSPAC)
T=0226 (839/3708,TWINSUK)
chr1:18729888 (GRCh38.p7) (1p36.13)
AD
GWASdb2
1   publication(s)
See rs on genome
33 Enhancers around
5 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.18729888C>T
GRCh37.p13 chr 1NC_000001.10:g.19056382C>T
PAX7 RefSeqGeneNG_023262.1:g.103883C>T

Gene: PAX7, paired box 7(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PAX7 transcript variant 3NM_001135254.1:c.N/AIntron Variant
PAX7 transcript variant 1NM_002584.2:c.N/AIntron Variant
PAX7 transcript variant 2NM_013945.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.586T=0.414
1000GenomesAmericanSub694C=0.830T=0.170
1000GenomesEast AsianSub1008C=0.920T=0.080
1000GenomesEuropeSub1006C=0.733T=0.267
1000GenomesGlobalStudy-wide5008C=0.739T=0.261
1000GenomesSouth AsianSub978C=0.700T=0.300
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.780T=0.220
The Genome Aggregation DatabaseAfricanSub8672C=0.606T=0.394
The Genome Aggregation DatabaseAmericanSub838C=0.780T=0.220
The Genome Aggregation DatabaseEast AsianSub1618C=0.928T=0.072
The Genome Aggregation DatabaseEuropeSub18432C=0.760T=0.239
The Genome Aggregation DatabaseGlobalStudy-wide29862C=0.723T=0.276
The Genome Aggregation DatabaseOtherSub302C=0.550T=0.450
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.700T=0.299
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.774T=0.226
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
rs27431890.000691alcohol dependence21314694

eQTL of rs2743189 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 rs2743189 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 )
chr11905007119050127E070-6255
chr11905028819050445E070-5937
chr11905057619050789E070-5593
chr11905140219051503E070-4879
chr11905167619051811E070-4571
chr11905183719052076E070-4306
chr11905213919053146E070-3236
chr11906628019066682E0709898
chr11908899119089140E07032609
chr11908950119089665E07233119
chr11904980319049884E081-6498
chr11905007119050127E081-6255
chr11905028819050445E081-5937
chr11905057619050789E081-5593
chr11905140219051503E081-4879
chr11905167619051811E081-4571
chr11905183719052076E081-4306
chr11905213919053146E081-3236
chr11906628019066682E0819898
chr11907369519073760E08117313
chr11907415819074593E08117776
chr11907463819074740E08118256
chr11909512719095274E08138745
chr11909548819095547E08139106
chr11909561219095868E08139230
chr11904980319049884E082-6498
chr11905007119050127E082-6255
chr11905028819050445E082-5937
chr11905057619050789E082-5593
chr11905140219051503E082-4879
chr11905167619051811E082-4571
chr11905183719052076E082-4306
chr11905213919053146E082-3236




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11904305719043267E070-13115
chr11904333219043792E070-12590
chr11904305719043267E082-13115
chr11904333219043792E082-12590
chr11904393519043994E082-12388