rs1004792

Homo sapiens
G>A
MMP25 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0192 (5618/29118,TOPMED)
A=0171 (858/5008,1000G)
A=0251 (969/3854,ALSPAC)
A=0239 (888/3708,TWINSUK)
chr16:3044260 (GRCh38.p7) (16p13.3)
AD
GWASdb2
2   publication(s)
See rs on genome
3 Enhancers around
39 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.3044260G>A
GRCh37.p13 chr 16NC_000016.9:g.3094261G>A

Gene: MMP25, matrix metallopeptidase 25(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
MMP25 transcriptNM_022468.4:c.N/AN/A
MMP25 transcript variant X4XM_017023561.1:c.N/AUpstream Transcript Variant
MMP25 transcript variant X1XM_011522602.2:c.N/AN/A
MMP25 transcript variant X3XM_011522604.2:c.N/AN/A
MMP25 transcript variant X5XM_011522605.2:c.N/AN/A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.891A=0.109
1000GenomesAmericanSub694G=0.840A=0.160
1000GenomesEast AsianSub1008G=0.868A=0.132
1000GenomesEuropeSub1006G=0.761A=0.239
1000GenomesGlobalStudy-wide5008G=0.829A=0.171
1000GenomesSouth AsianSub978G=0.770A=0.230
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.749A=0.251
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.807A=0.192
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.761A=0.239
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
19834535Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.Wheeler HEPLoS Genet

P-Value

SNP ID p-value Traits Study
rs10047920.0005alcohol dependence(early age of onset)20201924
rs10047920.00069alcohol dependence20201924

eQTL of rs1004792 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr16:3094261RP11-473M20.5ENSG00000205890.3G>A3.4121e-49362Cerebellum

meQTL of rs1004792 in Fetal Brain

Probe ID Position Gene beta p-value
cg00456894chr16:3096092MMP250.004713345761506341.4602e-17

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 )
chr1630686923068840E068-25421
chr1631074013107451E08113140
chr1631075333107857E08113272


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1630536293054347E067-39914
chr1630544053054591E067-39670
chr1630547103054817E067-39444
chr1630548363055245E067-39016
chr1631079443110347E06713683
chr1630536293054347E068-39914
chr1630544053054591E068-39670
chr1630547103054817E068-39444
chr1630548363055245E068-39016
chr1631079443110347E06813683
chr1631149473116230E06820686
chr1630536293054347E069-39914
chr1630544053054591E069-39670
chr1630547103054817E069-39444
chr1630548363055245E069-39016
chr1631079443110347E06913683
chr1630536293054347E070-39914
chr1630547103054817E070-39444
chr1630548363055245E070-39016
chr1631079443110347E07013683
chr1630536293054347E071-39914
chr1630544053054591E071-39670
chr1630547103054817E071-39444
chr1630548363055245E071-39016
chr1631079443110347E07113683
chr1631149473116230E07120686
chr1630536293054347E072-39914
chr1630544053054591E072-39670
chr1630547103054817E072-39444
chr1630548363055245E072-39016
chr1631079443110347E07213683
chr1630536293054347E073-39914
chr1630547103054817E073-39444
chr1630548363055245E073-39016
chr1631079443110347E07313683
chr1631079443110347E07413683
chr1630536293054347E082-39914
chr1630544053054591E082-39670
chr1631079443110347E08213683