Variant report

Variant	rs6078143
Chromosome Location	chr20:11351423-11351424
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	chr20:11351053..11352921-chr20:11353499..11355342,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11696977	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11698064	0.93[EUR][1000 genomes]
rs13038948	0.91[EUR][1000 genomes]
rs13043539	0.98[EUR][1000 genomes]
rs1535072	0.98[EUR][1000 genomes]
rs17800232	0.88[EUR][1000 genomes]
rs1997876	0.84[EUR][1000 genomes]
rs1997877	0.84[EUR][1000 genomes]
rs2327399	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28479511	0.99[EUR][1000 genomes]
rs6033095	0.84[EUR][1000 genomes]
rs6040515	0.84[EUR][1000 genomes]
rs6074279	0.88[EUR][1000 genomes]
rs6074281	0.88[EUR][1000 genomes]
rs6074283	0.91[EUR][1000 genomes]
rs6074287	0.99[EUR][1000 genomes]
rs6078118	0.84[EUR][1000 genomes]
rs6078132	0.87[EUR][1000 genomes]
rs6078136	0.88[EUR][1000 genomes]
rs6078138	0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6078141	0.99[EUR][1000 genomes]
rs6104738	0.93[EUR][1000 genomes]
rs6104739	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6108906	0.85[EUR][1000 genomes]
rs6108909	0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3409706	chr20:11347552-11352350	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a
5	esv3388930	chr20:11348452-11351550	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
6	esv3376008	chr20:11348452-11351650	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv3432469	chr20:11348552-11351550	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11335000-11355400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:11345400-11360000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:11346600-11358600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:11346800-11360000	Weak transcription	Psoas Muscle	Psoas
5	chr20:11347800-11356000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:11348000-11354400	Weak transcription	HMEC	breast
7	chr20:11349600-11352000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr20:11349800-11353200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:11350000-11353800	Weak transcription	Right Atrium	heart
10	chr20:11350400-11352800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:11350400-11353200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:11350400-11353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:11350400-11353800	Weak transcription	Esophagus	oesophagus
14	chr20:11350400-11356600	Weak transcription	Fetal Kidney	kidney
15	chr20:11350400-11360200	Weak transcription	Pancreas	Pancrea
16	chr20:11350600-11353200	Weak transcription	Fetal Brain Male	brain
17	chr20:11350600-11353600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr20:11351000-11353200	Weak transcription	Brain Germinal Matrix	brain
19	chr20:11351200-11358600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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