Variant report

Variant	rs2459220
Chromosome Location	chr4:56270472-56270473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56261651..56266514-chr4:56267808..56271520,10	MCF-7	breast:
2	chr4:56269662..56272449-chr4:56297179..56299575,2	K562	blood:
3	chr4:56210761..56214527-chr4:56265668..56271169,8	K562	blood:
4	chr4:56269741..56272367-chr4:56273938..56276057,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128039	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs471546	0.89[ASN][1000 genomes]
rs480531	0.83[AFR][1000 genomes]
rs4864984	0.89[ASN][1000 genomes]
rs491381	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs504836	0.89[ASN][1000 genomes]
rs505861	0.89[ASN][1000 genomes]
rs532768	0.89[ASN][1000 genomes]
rs534654	0.89[ASN][1000 genomes]
rs549564	0.89[ASN][1000 genomes]
rs566240	0.89[ASN][1000 genomes]
rs6554276	0.89[ASN][1000 genomes]
rs711533	0.89[ASN][1000 genomes]
rs73236137	0.89[ASN][1000 genomes]
rs7663955	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7664496	0.89[ASN][1000 genomes]
rs7692795	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv3513387	chr4:56265445-56270643	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56264200-56273000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:56264800-56282200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:56265000-56273200	Weak transcription	Gastric	stomach
5	chr4:56265400-56273400	Weak transcription	Aorta	Aorta
6	chr4:56265600-56271400	Weak transcription	Psoas Muscle	Psoas
7	chr4:56265600-56271800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:56265600-56272000	Weak transcription	Esophagus	oesophagus
9	chr4:56265600-56272200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:56265600-56273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:56265600-56273800	Weak transcription	Stomach Mucosa	stomach
12	chr4:56265600-56275600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:56265600-56281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:56265600-56283800	Weak transcription	Fetal Brain Male	brain
15	chr4:56265600-56286000	Weak transcription	Colonic Mucosa	Colon
16	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:56265800-56271400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:56265800-56271600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:56265800-56271600	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:56265800-56274400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:56265800-56275200	Weak transcription	Fetal Heart	heart
23	chr4:56265800-56281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:56266000-56270600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:56266000-56271800	Weak transcription	Fetal Brain Female	brain
26	chr4:56266000-56272000	Weak transcription	Brain Germinal Matrix	brain
27	chr4:56266000-56283200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:56266200-56275600	Weak transcription	Right Ventricle	heart
29	chr4:56266400-56271800	Weak transcription	Ovary	ovary
30	chr4:56266400-56272800	Weak transcription	Pancreas	Pancrea
31	chr4:56266600-56274200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:56267400-56270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:56267400-56271800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:56267400-56272000	Weak transcription	Brain Angular Gyrus	brain
35	chr4:56267400-56274200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:56267400-56275200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:56267400-56280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:56267400-56282800	Weak transcription	Small Intestine	intestine
39	chr4:56267400-56283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:56267600-56275800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:56267600-56280800	Weak transcription	A549	lung
42	chr4:56267800-56273400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:56268800-56272800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:56269000-56272400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:56269000-56273200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:56269000-56273600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr4:56269000-56274400	Strong transcription	HSMM	muscle
49	chr4:56269000-56311400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:56269200-56270600	Strong transcription	HSMMtube	muscle

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