rs1006438

Homo sapiens
T>C / T>G
LOC101927556 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0153 (4601/29966,GnomAD)
C=0191 (5562/29118,TOPMED)
C=0212 (1062/5008,1000G)
C=0070 (271/3854,ALSPAC)
C=0074 (273/3708,TWINSUK)
chr16:58138699 (GRCh38.p7) (16q21)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.58138699T>C
GRCh38.p7 chr 16NC_000016.10:g.58138699T>G
GRCh37.p13 chr 16NC_000016.9:g.58172603T>C
GRCh37.p13 chr 16NC_000016.9:g.58172603T>G

Gene: LOC101927556, uncharacterized LOC101927556(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC101927556 transcript variant X4XR_001752222.1:n....XR_001752222.1:n.578T>CT>CNon Coding Transcript Variant
LOC101927556 transcript variant X4XR_001752222.1:n....XR_001752222.1:n.578T>GT>GNon Coding Transcript Variant
LOC101927556 transcript variant X3XR_243455.4:n.N/AIntron Variant
LOC101927556 transcript variant X1XR_933632.2:n.N/AIntron Variant
LOC101927556 transcript variant X2XR_933633.2:n.N/AIntron Variant
LOC101927556 transcript variant X5XR_933634.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.656C=0.344
1000GenomesAmericanSub694T=0.840C=0.160
1000GenomesEast AsianSub1008T=0.644C=0.356
1000GenomesEuropeSub1006T=0.941C=0.059
1000GenomesGlobalStudy-wide5008T=0.788C=0.212
1000GenomesSouth AsianSub978T=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.930C=0.070
The Genome Aggregation DatabaseAfricanSub8714T=0.694C=0.306
The Genome Aggregation DatabaseAmericanSub838T=0.870C=0.130
The Genome Aggregation DatabaseEast AsianSub1616T=0.637C=0.363
The Genome Aggregation DatabaseEuropeSub18496T=0.935C=0.064
The Genome Aggregation DatabaseGlobalStudy-wide29966T=0.846C=0.153
The Genome Aggregation DatabaseOtherSub302T=0.860C=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.809C=0.191
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.926C=0.074
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
rs10064380.000781alcohol dependence21314694

eQTL of rs1006438 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 rs1006438 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.