rs12006002

Homo sapiens
C>T
ADAMTSL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0292 (8723/29852,GnomAD)
T=0292 (8505/29118,TOPMED)
T=0267 (1336/5008,1000G)
T=0335 (1290/3854,ALSPAC)
T=0322 (1194/3708,TWINSUK)
chr9:18166901 (GRCh38.p7) (9p22.2)
AD
GWASdb2
1   publication(s)
See rs on genome
16 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.18166901C>T
GRCh37.p13 chr 9NC_000009.11:g.18166899C>T

Gene: ADAMTSL1, ADAMTS like 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ADAMTSL1 transcript variant 4NM_001040272.5:c.N/AGenic Upstream Transcript Variant
ADAMTSL1 transcript variant 2NM_052866.4:c.N/AGenic Upstream Transcript Variant
ADAMTSL1 transcript variant X1XM_011518063.2:c.N/AIntron Variant
ADAMTSL1 transcript variant X3XM_011518064.2:c.N/AIntron Variant
ADAMTSL1 transcript variant X2XM_017015310.1:c.N/AIntron Variant
ADAMTSL1 transcript variant X4XM_017015311.1:c.N/AIntron Variant
ADAMTSL1 transcript variant X5XM_017015312.1:c.N/AIntron Variant
ADAMTSL1 transcript variant X7XM_017015314.1:c.N/AIntron Variant
ADAMTSL1 transcript variant X8XM_011518067.1:c.N/AGenic Upstream Transcript Variant
ADAMTSL1 transcript variant X9XM_011518068.2:c.N/AGenic Upstream Transcript Variant
ADAMTSL1 transcript variant X10XM_011518070.2:c.N/AGenic Upstream Transcript Variant
ADAMTSL1 transcript variant X6XM_017015313.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.783T=0.217
1000GenomesAmericanSub694C=0.590T=0.410
1000GenomesEast AsianSub1008C=0.848T=0.152
1000GenomesEuropeSub1006C=0.710T=0.290
1000GenomesGlobalStudy-wide5008C=0.733T=0.267
1000GenomesSouth AsianSub978C=0.670T=0.330
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.665T=0.335
The Genome Aggregation DatabaseAfricanSub8716C=0.746T=0.254
The Genome Aggregation DatabaseAmericanSub828C=0.490T=0.510
The Genome Aggregation DatabaseEast AsianSub1568C=0.851T=0.149
The Genome Aggregation DatabaseEuropeSub18438C=0.687T=0.312
The Genome Aggregation DatabaseGlobalStudy-wide29852C=0.707T=0.292
The Genome Aggregation DatabaseOtherSub302C=0.730T=0.270
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.707T=0.292
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.678T=0.322
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
rs120060020.000000487alcohol dependence23089632
rs120060020.00000724alcohol dependence23089632

eQTL of rs12006002 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 rs12006002 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 )
chr91821300618213587E06746107
chr91818990018190629E06823001
chr91819078318190945E06823884
chr91818975718189811E07022858
chr91818981918189877E07022920
chr91818990018190629E07023001
chr91812692818127002E074-39897
chr91812703018127178E074-39721
chr91812719418127300E074-39599
chr91812741518127505E074-39394
chr91818990018190629E07423001
chr91812692818127002E081-39897
chr91812703018127178E081-39721
chr91812719418127300E081-39599
chr91812741518127505E081-39394
chr91812755618127809E081-39090