rs16860582

Homo sapiens
T>C
LAMC2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0049 (1470/29992,GnomAD)
C=0060 (1772/29118,TOPMED)
C=0083 (414/5008,1000G)
C=0043 (164/3854,ALSPAC)
C=0036 (135/3708,TWINSUK)
chr1:183221316 (GRCh38.p7) (1q25.3)
AD
GWASdb2
1   publication(s)
See rs on genome
39 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.183221316T>C
GRCh37.p13 chr 1NC_000001.10:g.183190451T>C
LAMC2 RefSeqGeneNG_007079.2:g.40053T>C

Gene: LAMC2, laminin subunit gamma 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LAMC2 transcript variant 1NM_005562.2:c.N/AIntron Variant
LAMC2 transcript variant 2NM_018891.2:c.N/AIntron Variant
LAMC2 transcript variant X1XM_017001273.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.910C=0.090
1000GenomesAmericanSub694T=0.960C=0.040
1000GenomesEast AsianSub1008T=0.920C=0.080
1000GenomesEuropeSub1006T=0.958C=0.042
1000GenomesGlobalStudy-wide5008T=0.917C=0.083
1000GenomesSouth AsianSub978T=0.860C=0.140
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.957C=0.043
The Genome Aggregation DatabaseAfricanSub8730T=0.924C=0.076
The Genome Aggregation DatabaseAmericanSub836T=0.900C=0.100
The Genome Aggregation DatabaseEast AsianSub1620T=0.931C=0.069
The Genome Aggregation DatabaseEuropeSub18504T=0.967C=0.032
The Genome Aggregation DatabaseGlobalStudy-wide29992T=0.951C=0.049
The Genome Aggregation DatabaseOtherSub302T=0.960C=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.939C=0.060
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.964C=0.036
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
rs168605820.000297alcohol dependence20201924

eQTL of rs16860582 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 rs16860582 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 )
chr1183187882183188475E068-1976
chr1183233548183233663E06843097
chr1183233782183233881E06843331
chr1183233548183233663E06943097
chr1183233782183233881E06943331
chr1183149384183150534E070-39917
chr1183187882183188475E070-1976
chr1183188497183188788E070-1663
chr1183233548183233663E07043097
chr1183233548183233663E07243097
chr1183233548183233663E07343097
chr1183233782183233881E07343331
chr1183148676183148825E081-41626
chr1183149384183150534E081-39917
chr1183179586183179718E081-10733
chr1183179831183180056E081-10395
chr1183183368183183966E081-6485
chr1183184306183184702E081-5749
chr1183185211183185307E081-5144
chr1183185693183185793E081-4658
chr1183185919183185969E081-4482
chr1183186094183186286E081-4165
chr1183187232183187695E081-2756
chr1183187882183188475E081-1976
chr1183188497183188788E081-1663
chr1183233548183233663E08143097
chr1183233782183233881E08143331
chr1183148676183148825E082-41626
chr1183149384183150534E082-39917
chr1183183368183183966E082-6485
chr1183184306183184702E082-5749
chr1183185211183185307E082-5144
chr1183185693183185793E082-4658
chr1183185919183185969E082-4482
chr1183186094183186286E082-4165
chr1183187232183187695E082-2756
chr1183187882183188475E082-1976
chr1183188497183188788E082-1663
chr1183188901183188981E082-1470







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1183154801183155687E068-34764
chr1183154801183155687E070-34764
chr1183154801183155687E071-34764
chr1183154801183155687E082-34764