Variant report

Variant	rs6554276
Chromosome Location	chr4:56233552-56233553
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56232345..56235244-chr4:56243502..56246293,2	MCF-7	breast:
2	chr4:56232185..56234848-chr4:56260725..56263709,2	K562	blood:
3	chr4:56232180..56234979-chr4:56245346..56247186,2	K562	blood:
4	chr4:56210569..56212326-chr4:56231301..56233768,2	K562	blood:
5	chr4:56231811..56234116-chr4:56261269..56264003,2	MCF-7	breast:

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11721546	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11724565	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11727586	0.82[EUR][1000 genomes]
rs11733128	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2459220	0.89[ASN][1000 genomes]
rs471546	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480531	0.82[ASN][1000 genomes]
rs4864984	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491381	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504836	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505861	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532768	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534654	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549564	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566240	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66630638	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs711533	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73236137	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663955	0.89[ASN][1000 genomes]
rs7664496	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669259	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7672647	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7673897	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7692795	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697835	0.93[EUR][1000 genomes];0.88[ASN][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	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

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213400-56233600	Weak transcription	Fetal Intestine Large	intestine
2	chr4:56213600-56242600	Weak transcription	Gastric	stomach
3	chr4:56213800-56233600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:56213800-56239000	Weak transcription	Brain Germinal Matrix	brain
5	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
6	chr4:56214000-56237800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr4:56214000-56241800	Weak transcription	Colonic Mucosa	Colon
8	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:56215000-56235400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:56219400-56238400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:56220800-56241400	Weak transcription	Primary T cells from cord blood	blood
12	chr4:56225600-56235400	Weak transcription	Right Ventricle	heart
13	chr4:56225600-56237800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:56225800-56235600	Weak transcription	Aorta	Aorta
15	chr4:56225800-56236800	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:56225800-56237400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:56225800-56238400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:56225800-56244800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:56225800-56244800	Weak transcription	Stomach Mucosa	stomach
20	chr4:56226000-56233800	Weak transcription	Left Ventricle	heart
21	chr4:56226000-56234400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:56226000-56236000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:56226000-56237200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:56226000-56238400	Weak transcription	Osteobl	bone
25	chr4:56226000-56238600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:56226000-56240400	Weak transcription	HSMM	muscle
27	chr4:56226000-56241200	Weak transcription	Esophagus	oesophagus
28	chr4:56226000-56245000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:56226000-56245000	Weak transcription	HSMMtube	muscle
30	chr4:56227800-56238400	Weak transcription	Placenta	Placenta
31	chr4:56228000-56244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:56228400-56234400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:56228400-56245400	Weak transcription	K562	blood
34	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:56229400-56237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:56229800-56234200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:56229800-56236800	Strong transcription	Dnd41	blood
38	chr4:56229800-56237000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:56229800-56237000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:56230000-56234000	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr4:56230200-56237000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:56230400-56235400	Weak transcription	Fetal Brain Male	brain
43	chr4:56230400-56242000	Weak transcription	Ovary	ovary
44	chr4:56230600-56233800	Weak transcription	Fetal Thymus	thymus
45	chr4:56230600-56235600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:56230600-56237800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:56230600-56239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:56230600-56239600	Weak transcription	Fetal Brain Female	brain
49	chr4:56230600-56240200	Weak transcription	Fetal Lung	lung
50	chr4:56230600-56241200	Weak transcription	Fetal Muscle Leg	muscle

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