Variant report

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:49347789..49349298-chr20:52984375..52987184,2	MCF-7	breast:
2	chr20:52979804..52981716-chr20:52983200..52985662,2	MCF-7	breast:
3	chr20:52984992..52985954-chr20:53263110..53264230,3	MCF-7	breast:
4	chr20:52983863..52986994-chr20:52995623..52998239,3	MCF-7	breast:
5	chr20:49347583..49351619-chr20:52982625..52987672,5	MCF-7	breast:
6	chr20:52982598..52985363-chr20:52985830..52988598,3	MCF-7	breast:
7	chr20:52983415..52985850-chr6:27858765..27861037,2	MCF-7	breast:
8	chr17:73511489..73512024-chr20:52984570..52985199,2	MCF-7	breast:
9	chr20:52977120..52978918-chr20:52982695..52985421,2	MCF-7	breast:
10	chr20:52982179..52987061-chr20:52989270..52993345,5	MCF-7	breast:

No data

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

rs_ID	r²[population]
rs1539515	0.85[EUR][1000 genomes]
rs16999560	0.87[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17224616	0.81[EUR][1000 genomes]
rs17224715	0.83[EUR][1000 genomes]
rs17317237	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2126677	0.87[EUR][1000 genomes]
rs55865213	0.87[EUR][1000 genomes]
rs56339826	0.87[EUR][1000 genomes]
rs6091858	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6091860	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6097931	0.83[EUR][1000 genomes]
rs6097942	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6097943	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6097950	0.87[EUR][1000 genomes]
rs73143321	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73143323	0.87[EUR][1000 genomes]
rs73145242	0.87[EUR][1000 genomes]
rs73145250	0.87[EUR][1000 genomes]
rs73145257	0.87[EUR][1000 genomes]
rs73145263	0.87[EUR][1000 genomes]
rs73145273	0.87[EUR][1000 genomes]
rs73145277	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6097944	ATP9A	cis	parietal	SCAN
rs6097944	TSHZ2	cis	parietal	SCAN
rs6097944	RBM38	cis	parietal	SCAN
rs6097944	ZNF217	cis	cerebellum	SCAN
rs6097944	KCNG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52976600-52985200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr20:52977600-52985200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:52977800-52985200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr20:52983400-52986200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr20:52983800-52985200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:52984600-52986000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr20:52984800-52985400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr20:52984800-52986000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr20:52984800-52986000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr20:52985000-52985800	Weak transcription	H9 Cell Line	embryonic stem cell

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