Variant report

No.	Distal block	Cell Line	Cell type
1	chr2:86652314..86654591-chr2:86664666..86667245,2	MCF-7	breast:
2	chr2:86664840..86667143-chr2:86695504..86697285,2	MCF-7	breast:
3	chr2:86658372..86661098-chr2:86664087..86666512,2	MCF-7	breast:
4	chr2:86665985..86667815-chr2:86739595..86741738,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHMP3-2	chr2:86664163-86667836	NONHSAT072102

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10178917	0.81[AMR][1000 genomes]
rs10180036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127034	0.95[ASN][1000 genomes]
rs1137684	0.81[EUR][1000 genomes]
rs12617075	0.87[AMR][1000 genomes]
rs12714186	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13035266	0.85[AMR][1000 genomes]
rs13383096	0.87[AMR][1000 genomes]
rs1465813	0.84[EUR][1000 genomes]
rs2241803	0.83[EUR][1000 genomes]
rs2292887	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2367237	0.81[AMR][1000 genomes]
rs2367574	0.84[EUR][1000 genomes]
rs3201448	0.80[EUR][1000 genomes]
rs3731812	0.81[EUR][1000 genomes]
rs3755002	0.83[EUR][1000 genomes]
rs3770058	0.84[EUR][1000 genomes]
rs4832282	0.87[AMR][1000 genomes]
rs62150269	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6725080	0.83[EUR][1000 genomes]
rs908791	0.85[AMR][1000 genomes]
rs958561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12714184	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86665400-86667800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:86665400-86667800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
3	chr2:86665800-86666800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:86665800-86667600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:86665800-86667800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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