rs2092029

Homo sapiens
C>T
HMGXB4 : 2KB Upstream Variant
LOC105373017 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0482 (14414/29902,GnomAD)
T=0460 (13391/29114,TOPMED)
T=0471 (2361/5008,1000G)
C==0314 (1211/3854,ALSPAC)
C==0315 (1168/3708,TWINSUK)
chr22:35256248 (GRCh38.p7) (22q12.3)
AD
GWASdb2
1   publication(s)
See rs on genome
17 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 22NC_000022.11:g.35256248C>T
GRCh37.p13 chr 22NC_000022.10:g.35652241C>T

Gene: HMGXB4, HMG-box containing 4(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
HMGXB4 transcript variant 1NM_001003681.2:c.N/AUpstream Transcript Variant
HMGXB4 transcript variant 2NR_027780.1:n.N/AUpstream Transcript Variant
HMGXB4 transcript variant X1XM_006724100.3:c.N/AUpstream Transcript Variant
HMGXB4 transcript variant X2XM_006724101.3:c.N/AUpstream Transcript Variant
HMGXB4 transcript variant X3XM_006724102.1:c.N/AUpstream Transcript Variant

Gene: LOC105373017, uncharacterized LOC105373017(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105373017 transcript variant X1XR_938209.2:n.N/AIntron Variant
LOC105373017 transcript variant X3XR_938210.2:n.N/AIntron Variant
LOC105373017 transcript variant X2XR_938211.1:n.N/AIntron Variant
LOC105373017 transcript variant X4XR_938212.2:n.N/AIntron Variant
LOC105373017 transcript variant X5XR_938213.2:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.900T=0.100
1000GenomesAmericanSub694C=0.390T=0.610
1000GenomesEast AsianSub1008C=0.477T=0.523
1000GenomesEuropeSub1006C=0.319T=0.681
1000GenomesGlobalStudy-wide5008C=0.529T=0.471
1000GenomesSouth AsianSub978C=0.390T=0.610
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.314T=0.686
The Genome Aggregation DatabaseAfricanSub8708C=0.816T=0.184
The Genome Aggregation DatabaseAmericanSub838C=0.380T=0.620
The Genome Aggregation DatabaseEast AsianSub1614C=0.449T=0.551
The Genome Aggregation DatabaseEuropeSub18442C=0.335T=0.664
The Genome Aggregation DatabaseGlobalStudy-wide29902C=0.482T=0.518
The Genome Aggregation DatabaseOtherSub300C=0.270T=0.730
Trans-Omics for Precision MedicineGlobalStudy-wide29114C=0.540T=0.460
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.315T=0.685
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs20920290.000447alcohol consumption (maxi-drinks)24277619

eQTL of rs2092029 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 rs2092029 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 )
chr223565492135655002E0692680
chr223565522735655271E0702986
chr223565550635655560E0703265
chr223565645335656503E0704212
chr223565492135655002E0712680
chr223565506035655153E0712819
chr223565492135655002E0722680
chr223565506035655153E0722819
chr223569895735699062E07246716
chr223569918335699267E07246942
chr223569930735699451E07247066
chr223565492135655002E0732680
chr223565506035655153E0732819
chr223565492135655002E0742680
chr223565506035655153E0822819
chr223565522735655271E0822986
chr223565550635655560E0823265







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr223565300235654849E067761
chr223569471735696911E06742476
chr223565300235654849E068761
chr223569471735696911E06842476
chr223565300235654849E069761
chr223569471735696911E06942476
chr223565300235654849E070761
chr223569471735696911E07042476
chr223565300235654849E071761
chr223569471735696911E07142476
chr223565300235654849E072761
chr223569471735696911E07242476
chr223565300235654849E073761
chr223569471735696911E07342476
chr223565300235654849E074761
chr223569471735696911E07442476
chr223565300235654849E081761
chr223569471735696911E08142476
chr223565300235654849E082761
chr223569471735696911E08242476