rs890793

Homo sapiens
C>G / C>T
GALNT10 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0354 (10606/29946,GnomAD)
T=0311 (9077/29118,TOPMED)
T=0443 (2221/5008,1000G)
T=0375 (1446/3854,ALSPAC)
T=0375 (1392/3708,TWINSUK)
chr5:154194378 (GRCh38.p7) (5q33.2)
AD
GWASdb2
1   publication(s)
See rs on genome
1 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.154194378C>G
GRCh38.p7 chr 5NC_000005.10:g.154194378C>T
GRCh37.p13 chr 5NC_000005.9:g.153573938C>G
GRCh37.p13 chr 5NC_000005.9:g.153573938C>T

Gene: GALNT10, polypeptide N-acetylgalactosaminyltransferase 10(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GALNT10 transcriptNM_198321.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.864T=0.136
1000GenomesAmericanSub694C=0.420T=0.580
1000GenomesEast AsianSub1008C=0.126T=0.874
1000GenomesEuropeSub1006C=0.615T=0.385
1000GenomesGlobalStudy-wide5008C=0.557T=0.443
1000GenomesSouth AsianSub978C=0.620T=0.380
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.625T=0.375
The Genome Aggregation DatabaseAfricanSub8716C=0.795G=0.000
The Genome Aggregation DatabaseAmericanSub836C=0.370G=0.00,
The Genome Aggregation DatabaseEast AsianSub1618C=0.125G=0.000
The Genome Aggregation DatabaseEuropeSub18474C=0.634G=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29946C=0.645G=0.000
The Genome Aggregation DatabaseOtherSub302C=0.580G=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.688T=0.311
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.625T=0.375
PMID Title Author Journal
23089632A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.Wang JCMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs8907931.1E-05alcohol dependence23089632

eQTL of rs890793 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 rs890793 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 )
chr56424292364243245E08127760