rs1800973

Homo sapiens
C>A
LYZ : Missense Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0042 (5186/121310,ExAC)
A=0044 (1321/29966,GnomAD)
A=0036 (1058/29118,TOPMED)
C==0050 (656/13006,GO-ESP)
A=0015 (73/5008,1000G)
A=0067 (260/3854,ALSPAC)
A=0059 (220/3708,TWINSUK)
chr12:69350234 (GRCh38.p7) (12q15)
AD
GWASdb2
4   publication(s)
See rs on genome
9 Enhancers around
16 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.69350234C>A
GRCh37.p13 chr 12NC_000012.11:g.69744014C>A
LYZ RefSeqGene LRG_768

Gene: LYZ, lysozyme(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LYZ transcriptNM_000239.2:c.263C>AT [ACC]> N [AAC]Coding Sequence Variant
lysozyme C precursorNP_000230.1:p.Thr...NP_000230.1:p.Thr88AsnT [Thr]> N [Asn]Missense Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.999A=0.001
1000GenomesAmericanSub694C=0.970A=0.030
1000GenomesEast AsianSub1008C=1.000A=0.000
1000GenomesEuropeSub1006C=0.956A=0.044
1000GenomesGlobalStudy-wide5008C=0.985A=0.015
1000GenomesSouth AsianSub978C=0.990A=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.933A=0.067
The Exome Aggregation ConsortiumAmericanSub21952C=0.985A=0.014
The Exome Aggregation ConsortiumAsianSub25156C=0.993A=0.006
The Exome Aggregation ConsortiumEuropeSub73294C=0.936A=0.063
The Exome Aggregation ConsortiumGlobalStudy-wide121310C=0.957A=0.042
The Exome Aggregation ConsortiumOtherSub908C=0.960A=0.040
The Genome Aggregation DatabaseAfricanSub8716C=0.989A=0.011
The Genome Aggregation DatabaseAmericanSub838C=0.970A=0.030
The Genome Aggregation DatabaseEast AsianSub1622C=1.000A=0.000
The Genome Aggregation DatabaseEuropeSub18488C=0.936A=0.063
The Genome Aggregation DatabaseGlobalStudy-wide29966C=0.955A=0.044
The Genome Aggregation DatabaseOtherSub302C=0.930A=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.963A=0.036
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.941A=0.059
PMID Title Author Journal
12709420Structural and folding dynamic properties of the T70N variant of human lysozyme.Esposito GJ Biol Chem
26547235Crowdsourced direct-to-consumer genomic analysis of a family quartet.Corpas MBMC Genomics
19581569Genome-wide association study of alcohol dependence.Treutlein JArch Gen Psychiatry
16329101ALys amyloidosis caused by compound heterozygosity in exon 2 (Thr70Asn) and exon 4 (Trp112Arg) of the lysozyme gene.Rocken CHum Mutat

P-Value

SNP ID p-value Traits Study
rs18009739.46E-07alcohol dependence19581569

eQTL of rs1800973 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 rs1800973 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 )
chr126975130669751701E0677292
chr126975130669751701E0687292
chr126977268669773039E06928672
chr126973465369734693E071-9321
chr126973476269734925E071-9089
chr126973493569735010E071-9004
chr126975130669751701E0727292
chr126977268669773039E07428672
chr126975542269755490E08211408







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr126975288369754507E0678869
chr126972361769725984E068-18030
chr126975288369754507E0688869
chr126975288369754507E0698869
chr126975288369754507E0708869
chr126972361769725984E071-18030
chr126974256669742708E071-1306
chr126975288369754507E0718869
chr126975266069752710E0728646
chr126975288369754507E0728869
chr126972361769725984E073-18030
chr126975288369754507E0738869
chr126972361769725984E074-18030
chr126975288369754507E0748869
chr126975288369754507E0818869
chr126975288369754507E0828869