Variant report

Variant	rs573960
Chromosome Location	chr4:56236804-56236805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56235460..56238150-chr4:56260336..56262058,2	MCF-7	breast:
2	chr4:56235502..56237300-chr4:56240402..56242379,2	K562	blood:
3	chr4:56235502..56237390-chr4:56239912..56242405,3	K562	blood:

Variant related genes	Relation type
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10010762	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10021233	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10024928	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1818460	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1961107	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609134	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4089487	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4455482	0.82[ASN][1000 genomes]
rs475465	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs476184	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs482114	0.82[AMR][1000 genomes]
rs483978	0.83[AMR][1000 genomes]
rs496055	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs499110	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs525271	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs552792	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs552950	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs556072	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs572553	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs576732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58506276	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62305200	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62305201	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62305202	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62305206	0.80[ASN][1000 genomes]
rs62306207	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6554275	0.81[EUR][1000 genomes]
rs7340797	0.81[EUR][1000 genomes]
rs819203	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs819266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs819267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs819268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs819269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs819270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861029	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9312660	0.83[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	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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213600-56242600	Weak transcription	Gastric	stomach
2	chr4:56213800-56239000	Weak transcription	Brain Germinal Matrix	brain
3	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
4	chr4:56214000-56237800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:56214000-56241800	Weak transcription	Colonic Mucosa	Colon
6	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:56219400-56238400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:56220800-56241400	Weak transcription	Primary T cells from cord blood	blood
9	chr4:56225600-56237800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:56225800-56237400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:56225800-56238400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:56225800-56244800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:56225800-56244800	Weak transcription	Stomach Mucosa	stomach
14	chr4:56226000-56237200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:56226000-56238400	Weak transcription	Osteobl	bone
16	chr4:56226000-56238600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:56226000-56240400	Weak transcription	HSMM	muscle
18	chr4:56226000-56241200	Weak transcription	Esophagus	oesophagus
19	chr4:56226000-56245000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:56226000-56245000	Weak transcription	HSMMtube	muscle
21	chr4:56227800-56238400	Weak transcription	Placenta	Placenta
22	chr4:56228000-56244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:56228400-56245400	Weak transcription	K562	blood
24	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:56229400-56237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:56229800-56237000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:56229800-56237000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr4:56230200-56237000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:56230400-56242000	Weak transcription	Ovary	ovary
30	chr4:56230600-56237800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:56230600-56239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:56230600-56239600	Weak transcription	Fetal Brain Female	brain
33	chr4:56230600-56240200	Weak transcription	Fetal Lung	lung
34	chr4:56230600-56241200	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:56230600-56245200	Weak transcription	Fetal Intestine Small	intestine
36	chr4:56231800-56237000	Weak transcription	Liver	Liver
37	chr4:56231800-56238400	Weak transcription	Thymus	Thymus
38	chr4:56232000-56238200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr4:56232000-56241800	Weak transcription	Lung	lung
40	chr4:56232000-56247600	Weak transcription	Spleen	Spleen
41	chr4:56233200-56238200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:56233200-56238400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:56233200-56241800	Weak transcription	Fetal Stomach	stomach
44	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:56233400-56239400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:56233600-56237000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:56233600-56237200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:56233600-56237600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:56233600-56237800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:56233600-56237800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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