Variant report

Variant	rs6050780
Chromosome Location	chr20:25654209-25654210
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25653186-25654721	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:25654192-25654541	MCF-7	breast:	n/a	n/a
3	POLR2A	chr20:25653624-25654761	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr20:25653783-25654258	GM12878	blood:	n/a	n/a
5	POLR2A	chr20:25653331-25654658	K562	blood:	n/a	n/a
6	SETDB1	chr20:25653876-25655064	U2OS	brain:	n/a	n/a
7	POLR2A	chr20:25653228-25654381	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr20:25653567-25654716	HepG2	liver:	n/a	n/a
9	POLR2A	chr20:25653616-25654811	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25604523..25606261-chr20:25653014..25654610,2	MCF-7	breast:
2	chr20:25603937..25605836-chr20:25653672..25656998,3	MCF-7	breast:
3	chr20:25652247..25655467-chr20:25656048..25658706,3	MCF-7	breast:

Variant related genes	Relation type
MED28P7	TF binding region
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2064276	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6037216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6037221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050826	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25605600-25654600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:25625000-25655200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:25649200-25655200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr20:25649400-25654400	Weak transcription	Fetal Kidney	kidney
5	chr20:25650600-25655000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:25650600-25655800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:25650600-25657000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:25651000-25654400	Weak transcription	HSMMtube	muscle
9	chr20:25651200-25654600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr20:25651200-25655000	Weak transcription	Colonic Mucosa	Colon
11	chr20:25651600-25659600	Strong transcription	Fetal Brain Female	brain
12	chr20:25651800-25655400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr20:25652000-25655600	Weak transcription	Fetal Heart	heart
14	chr20:25652000-25659600	Strong transcription	Brain Germinal Matrix	brain
15	chr20:25652200-25654600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr20:25652200-25655000	Weak transcription	GM12878-XiMat	blood
17	chr20:25652600-25654400	Weak transcription	Psoas Muscle	Psoas
18	chr20:25652600-25654800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr20:25652600-25658800	Strong transcription	Fetal Stomach	stomach
20	chr20:25653000-25655200	Weak transcription	Hela-S3	cervix
21	chr20:25653000-25657000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:25653000-25663600	Strong transcription	HSMM	muscle
23	chr20:25653200-25655800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr20:25653200-25656800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr20:25653200-25657400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr20:25653200-25657400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:25653200-25659600	Strong transcription	Fetal Intestine Small	intestine
28	chr20:25653200-25662800	Strong transcription	Fetal Lung	lung
29	chr20:25653400-25654400	Strong transcription	Fetal Brain Male	brain
30	chr20:25653400-25654800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr20:25653400-25655000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr20:25653400-25656800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr20:25653400-25656800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr20:25653400-25656800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:25653400-25656800	Strong transcription	NH-A	brain
36	chr20:25653400-25657000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr20:25653400-25657400	Strong transcription	A549	lung
38	chr20:25653400-25657600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr20:25653400-25657600	Strong transcription	Brain Substantia Nigra	brain
40	chr20:25653400-25657800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr20:25653400-25658200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr20:25653400-25658600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr20:25653400-25658800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr20:25653400-25659200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr20:25653400-25659400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr20:25653400-25659600	Strong transcription	Brain Angular Gyrus	brain
47	chr20:25653400-25659600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr20:25653400-25659600	Strong transcription	Ovary	ovary
49	chr20:25653400-25659600	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr20:25653400-25659600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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