rs12259062

Homo sapiens
A>G
HTR7 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0485 (14545/29958,GnomAD)
A==0444 (12950/29118,TOPMED)
A==0453 (2269/5008,1000G)
G=0332 (1278/3854,ALSPAC)
G=0327 (1214/3708,TWINSUK)
chr10:90850288 (GRCh38.p7) (10q23.31)
AD
GWASdb2
1   publication(s)
See rs on genome
18 Enhancers around
21 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.90850288A>G
GRCh37.p13 chr 10NC_000010.10:g.92610045A>G
HTR7 RefSeqGeneNG_029218.1:g.12627T>C

Gene: HTR7, 5-hydroxytryptamine receptor 7(minus strand)

Molecule type Change Amino acid[Codon] SO Term
HTR7 transcript variant aNM_000872.4:c.N/AIntron Variant
HTR7 transcript variant dNM_019859.3:c.N/AIntron Variant
HTR7 transcript variant bNM_019860.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.085G=0.915
1000GenomesAmericanSub694A=0.570G=0.430
1000GenomesEast AsianSub1008A=0.573G=0.427
1000GenomesEuropeSub1006A=0.639G=0.361
1000GenomesGlobalStudy-wide5008A=0.453G=0.547
1000GenomesSouth AsianSub978A=0.550G=0.450
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.668G=0.332
The Genome Aggregation DatabaseAfricanSub8724A=0.172G=0.828
The Genome Aggregation DatabaseAmericanSub838A=0.570G=0.430
The Genome Aggregation DatabaseEast AsianSub1612A=0.547G=0.453
The Genome Aggregation DatabaseEuropeSub18482A=0.668G=0.331
The Genome Aggregation DatabaseGlobalStudy-wide29958A=0.514G=0.485
The Genome Aggregation DatabaseOtherSub302A=0.660G=0.340
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.444G=0.555
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.673G=0.327
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
rs122590620.00063alcohol consumption (maxi-drinks)24277619

eQTL of rs12259062 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 rs12259062 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 )
chr109263305792633097E06723012
chr109263338892633438E06723343
chr109263358692633643E06723541
chr109263401892634073E06723973
chr109263305792633097E06923012
chr109263338892633438E06923343
chr109263358692633643E06923541
chr109263305792633097E07023012
chr109263358692633643E07023541
chr109263305792633097E07323012
chr109263338892633438E07323343
chr109263358692633643E07323541
chr109263305792633097E08123012
chr109263338892633438E08123343
chr109263358692633643E08123541
chr109263338892633438E08223343
chr109263358692633643E08223541
chr109263401892634073E08223973






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr109261595792618611E0675912
chr109263077892632583E06720733
chr109261595792618611E0685912
chr109263077892632583E06820733
chr109261595792618611E0695912
chr109263077892632583E06920733
chr109263077892632583E07020733
chr109261595792618611E0715912
chr109263077892632583E07120733
chr109261595792618611E0725912
chr109263077892632583E07220733
chr109261595792618611E0735912
chr109263077892632583E07320733
chr109261595792618611E0745912
chr109263077892632583E07420733
chr109263077892632583E08120733
chr109261475592614846E0824710
chr109261555192615609E0825506
chr109261574592615805E0825700
chr109261595792618611E0825912
chr109263077892632583E08220733