Variant report

Variant	rs12685086
Chromosome Location	chr9:95647120-95647121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95638865..95641445-chr9:95646989..95649985,2	MCF-7	breast:
2	chr9:95630810..95632810-chr9:95646965..95649484,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127081	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10761181	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821036	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821037	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992512	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992513	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11792027	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12003227	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16905839	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1966189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980698	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2146718	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2281715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281716	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281717	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4076629	0.82[AMR][1000 genomes]
rs4076630	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62572398	0.82[AMR][1000 genomes]
rs7030886	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7044372	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7847040	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]

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	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv893574	chr9:95580376-95688099	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv972781	chr9:95639258-95671744	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
4	nsv982544	chr9:95644425-95647585	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12685086	ZNF484	cis	cerebellum	SCAN
rs12685086	SUSD3	cis	multi-tissue	Pritchard
rs12685086	ZNF484	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95640600-95648800	Weak transcription	Thymus	Thymus
2	chr9:95640800-95647800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:95640800-95648600	Weak transcription	Primary T cells from cord blood	blood
4	chr9:95640800-95648600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:95641000-95648400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:95644600-95647200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:95645800-95647200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr9:95646600-95648200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr9:95646600-95648800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:95646800-95648400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr9:95646800-95649000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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