rs10952334

Homo sapiens
G>C
GALNTL5 : Non Coding Transcript Variant
LOC105375570 : 2KB Upstream Variant
LOC105375571 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0275 (8220/29884,GnomAD)
G==0299 (8725/29118,TOPMED)
G==0286 (1432/5008,1000G)
G==0277 (1066/3854,ALSPAC)
G==0283 (1050/3708,TWINSUK)
chr7:151956550 (GRCh38.p7) (7q36.1)
AD
GWASdb2
1   publication(s)
See rs on genome
18 Enhancers around
1 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.151956550G>C
GRCh37.p13 chr 7NC_000007.13:g.151653635G>C

Gene: GALNTL5, polypeptide N-acetylgalactosaminyltransferase-like 5(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GALNTL5 transcript variant 1NM_145292.3:c.N/A5 Prime UTR Variant
GALNTL5 transcript variant 2NR_033169.1:n.172G>CG>CNon Coding Transcript Variant
GALNTL5 transcript variant X2XM_006715862.3:c.N/A5 Prime UTR Variant
GALNTL5 transcript variant X3XM_011515849.2:c.N/AGenic Upstream Transcript Variant
GALNTL5 transcript variant X4XM_011515852.2:c.N/AGenic Upstream Transcript Variant
GALNTL5 transcript variant X5XM_011515853.2:c.N/AGenic Upstream Transcript Variant
GALNTL5 transcript variant X1XM_017011793.1:c.N/AGenic Upstream Transcript Variant
GALNTL5 transcript variant X6XM_017011794.1:c.N/AGenic Upstream Transcript Variant
GALNTL5 transcript variant X8XM_017011795.1:c.N/AGenic Upstream Transcript Variant
GALNTL5 transcript variant X9XM_017011796.1:c.N/AGenic Upstream Transcript Variant
GALNTL5 transcript variant X7XR_001744572.1:n.N/AGenic Upstream Transcript Variant

Gene: LOC105375570, uncharacterized LOC105375570(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC105375570 transcriptXR_928178.2:n.N/AUpstream Transcript Variant

Gene: LOC105375571, uncharacterized LOC105375571(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC105375571 transcriptXR_928179.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.294C=0.706
1000GenomesAmericanSub694G=0.240C=0.760
1000GenomesEast AsianSub1008G=0.390C=0.610
1000GenomesEuropeSub1006G=0.230C=0.770
1000GenomesGlobalStudy-wide5008G=0.286C=0.714
1000GenomesSouth AsianSub978G=0.260C=0.740
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.277C=0.723
The Genome Aggregation DatabaseAfricanSub8690G=0.316C=0.684
The Genome Aggregation DatabaseAmericanSub834G=0.200C=0.800
The Genome Aggregation DatabaseEast AsianSub1610G=0.386C=0.614
The Genome Aggregation DatabaseEuropeSub18448G=0.249C=0.750
The Genome Aggregation DatabaseGlobalStudy-wide29884G=0.275C=0.724
The Genome Aggregation DatabaseOtherSub302G=0.320C=0.680
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.299C=0.700
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.283C=0.717
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
rs109523340.000781alcohol dependence21314694

eQTL of rs10952334 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 rs10952334 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 )
chr7151622573151623640E068-29995
chr7151629283151629998E068-23637
chr7151689342151689875E06835707
chr7151620734151620944E069-32691
chr7151620987151621138E069-32497
chr7151622573151623640E069-29995
chr7151621249151621303E071-32332
chr7151621319151621454E071-32181
chr7151622573151623640E071-29995
chr7151623687151623780E071-29855
chr7151689342151689875E07135707
chr7151622573151623640E073-29995
chr7151614796151615557E074-38078
chr7151615589151615662E074-37973
chr7151615711151615816E074-37819
chr7151622236151622345E074-31290
chr7151622573151623640E081-29995
chr7151689342151689875E08135707






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr7151652097151652894E068-741