Variant report

Variant	rs7025712
Chromosome Location	chr9:8269073-8269074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10815816	0.82[AMR][1000 genomes]
rs10815818	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10976892	0.94[ASN][1000 genomes]
rs10976895	0.83[ASN][1000 genomes]
rs10976903	0.81[AFR][1000 genomes]
rs10976910	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976915	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10976918	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12551280	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12555489	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12685816	0.82[EUR][1000 genomes]
rs1500306	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1546256	0.86[AMR][1000 genomes]
rs16927434	0.84[EUR][1000 genomes]
rs3847282	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3847283	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3847284	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3858056	0.86[AFR][1000 genomes]
rs4008238	0.81[EUR][1000 genomes]
rs7031618	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7042696	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7860201	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7864066	0.81[EUR][1000 genomes]
rs950832	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9785185	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv613284	chr9:8165192-8279622	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	inside rSNPs	diseases
3	nsv1016723	chr9:8223541-8303017	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
4	nsv613285	chr9:8244354-8270248	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	nsv466123	chr9:8247628-8270248	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
6	nsv613286	chr9:8247628-8270248	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
7	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv892223	chr9:8258921-8318948	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	miRNA target site	n/a	inside rSNPs	diseases
9	nsv892224	chr9:8263737-8338431	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7025712	C1orf220	trans	cerebellum	SCAN
rs7025712	FIG4	trans	parietal	SCAN
rs7025712	STAP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8264400-8274800	Weak transcription	Fetal Intestine Small	intestine
2	chr9:8265400-8270600	Enhancers	Fetal Lung	lung
3	chr9:8267600-8269800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr9:8267800-8269200	Enhancers	Pancreas	Pancrea
5	chr9:8267800-8269200	Enhancers	Stomach Smooth Muscle	stomach
6	chr9:8267800-8269800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:8267800-8269800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:8267800-8269800	Enhancers	Psoas Muscle	Psoas
9	chr9:8268400-8269200	Bivalent Enhancer	Small Intestine	intestine
10	chr9:8268800-8271000	Enhancers	Stomach Mucosa	stomach

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