rs12473275

Homo sapiens
G>A
ALK : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0149 (4357/29116,TOPMED)
A=0199 (996/5008,1000G)
A=0101 (391/3854,ALSPAC)
A=0115 (427/3708,TWINSUK)
chr2:29562915 (GRCh38.p7) (2p23.2)
AD
GWASdb2
1   publication(s)
See rs on genome
22 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.29562915G>A
GRCh37.p13 chr 2NC_000002.11:g.29785781G>A
ALK RefSeqGene LRG_488

Gene: ALK, anaplastic lymphoma receptor tyrosine kinase(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ALK transcript variant 1NM_004304.4:c.N/AIntron Variant
ALK transcript variant X1XR_001738688.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.796A=0.204
1000GenomesAmericanSub694G=0.770A=0.230
1000GenomesEast AsianSub1008G=0.720A=0.280
1000GenomesEuropeSub1006G=0.894A=0.106
1000GenomesGlobalStudy-wide5008G=0.801A=0.199
1000GenomesSouth AsianSub978G=0.820A=0.180
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.899A=0.101
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.850A=0.149
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.885A=0.115
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs124732756.11E-05alcohol dependence21703634

eQTL of rs12473275 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 rs12473275 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 )
chr22975165629752357E068-33424
chr22979868729798775E06912906
chr22974026829740645E070-45136
chr22974091429741266E070-44515
chr22979855229798611E07012771
chr22979868729798775E07012906
chr22979893029799416E07013149
chr22980272029802911E07016939
chr22980292529802985E07017144
chr22980308929803371E07017308
chr22980600529806284E07120224
chr22978408129784335E081-1446
chr22978446529784583E081-1198
chr22980253229802589E08116751
chr22980272029802911E08116939
chr22980292529802985E08117144
chr22980308929803371E08117308
chr22975165629752357E082-33424
chr22979088529791085E0825104
chr22979118529791253E0825404
chr22980272029802911E08216939
chr22980292529802985E08217144