rs3747443

Homo sapiens
A>G
CXorf40A : Intron Variant
LINC00893 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0172 (3517/20402,GnomAD)
G==0176 (664/3775,1000G)
G==0076 (281/3708,TWINSUK)
G==0085 (247/2889,ALSPAC)
chrX:149541185 (GRCh38.p7) (Xq28)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr XNC_000023.11:g.149541185A>G
GRCh37.p13 chr X fix patch HG1459_PATCHNW_004070890.2:g.5065583A>G
GRCh37.p13 chr XNC_000023.10:g.148622730G>A

Gene: CXorf40A, chromosome X open reading frame 40A(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CXorf40A transcript variant 5NM_001324274.1:c.N/AIntron Variant
CXorf40A transcript variant 6NM_001324275.1:c.N/AIntron Variant
CXorf40A transcript variant 1NM_178124.5:c.N/A5 Prime UTR Variant
CXorf40A transcript variant 3NM_001171908.2:c.N/A5 Prime UTR Variant
CXorf40A transcript variant 2NM_001171907.2:c.N/A5 Prime UTR Variant
CXorf40A transcript variant 11NM_001324280.1:c.N/A5 Prime UTR Variant
CXorf40A transcript variant 8NM_001324277.1:c.N/A5 Prime UTR Variant
CXorf40A transcript variant 9NM_001324278.1:c.N/A5 Prime UTR Variant
CXorf40A transcript variant 10NM_001324279.1:c.N/A5 Prime UTR Variant
CXorf40A transcript variant 7NM_001324276.1:c.N/A5 Prime UTR Variant
CXorf40A transcript variant 4NM_001171909.3:c.N/AGenic Upstream Transcript Variant
CXorf40A transcript variant X1XM_005262349.4:c.N/AGenic Upstream Transcript Variant

Gene: LINC00893, long intergenic non-protein coding RNA 893(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LINC00893 transcriptNR_027455.5:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1003G=0.443A==0.557
1000GenomesAmericanSub524G=0.060A==0.940
1000GenomesEast AsianSub764G=0.100A==0.900
1000GenomesEuropeSub766G=0.080A==0.920
1000GenomesGlobalStudy-wide3775G=0.176A==0.824
1000GenomesSouth AsianSub718G=0.070A==0.930
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide2889G=0.085A==0.915
The Genome Aggregation DatabaseAfricanSub5669G=0.415A==0.585
The Genome Aggregation DatabaseAmericanSub617G=0.070A==0.930
The Genome Aggregation DatabaseEast AsianSub1014G=0.056A==0.944
The Genome Aggregation DatabaseEuropeSub12915G=0.081A==0.918
The Genome Aggregation DatabaseGlobalStudy-wide20402G=0.172A==0.827
The Genome Aggregation DatabaseOtherSub187G=0.090A==0.910
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.076A==0.924
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs37474430.00079alcohol dependence20201924

eQTL of rs3747443 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
ChrX:148622730TMEM185AENSG00000155984.10G>A1.8424e-15-90838Cerebellum
ChrX:148622730TMEM185AENSG00000155984.10G>A1.0735e-8-90838Frontal_Cortex_BA9
ChrX:148622730TMEM185AENSG00000155984.10G>A7.3132e-8-90838Cortex
ChrX:148622730TMEM185AENSG00000155984.10G>A6.7764e-10-90838Cerebellar_Hemisphere
ChrX:148622730TMEM185AENSG00000155984.10G>A9.1826e-5-90838Caudate_basal_ganglia
ChrX:148622730TMEM185AENSG00000155984.10G>A9.6647e-6-90838Brain_Spinal_cord_cervical
ChrX:148622730TMEM185AENSG00000155984.10G>A1.0019e-5-90838Anterior_cingulate_cortex
ChrX:148622730TMEM185AENSG00000155984.10G>A5.3948e-9-90838Nucleus_accumbens_basal_ganglia

meQTL of rs3747443 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.