Variant report

Variant	rs1860372
Chromosome Location	chr12:47185417-47185418
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10161209	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11183618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183619	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12300935	0.82[ASN][1000 genomes]
rs12305532	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306007	0.81[CHB][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12318924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581848	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17097332	0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs180431	0.88[CHB][hapmap]
rs1860371	0.88[AFR][1000 genomes]
rs2079787	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2465585	0.89[YRI][hapmap]
rs2465604	0.80[YRI][hapmap]
rs2715788	0.89[YRI][hapmap]
rs3862137	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482114	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1860372	MMP21	trans	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47164200-47187800	Genic enhancers	Liver	Liver
2	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney
3	chr12:47179000-47189800	Weak transcription	Fetal Lung	lung
4	chr12:47181000-47194200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:47181800-47185600	Weak transcription	Pancreas	Pancrea
6	chr12:47182400-47187200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:47182400-47187400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:47182400-47194200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:47182600-47188600	Weak transcription	HepG2	liver
10	chr12:47183400-47187400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:47184800-47186200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:47185000-47192200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:47185200-47185800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:47185200-47186400	Strong transcription	HSMM	muscle
15	chr12:47185400-47186200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:47185400-47186800	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr12:47185400-47187000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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