Variant report

Variant	rs56371028
Chromosome Location	chr4:77173476-77173477
allele	C/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	USF2	chr4:77173441-77173486	H1-hESC	embryonic stem cell:	n/a	n/a
2	EP300	chr4:77173213-77173483	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr4:77173066-77173517	SK-N-SH_RA	brain:	n/a	n/a
4	YY1	chr4:77172536-77173497	H1-hESC	embryonic stem cell:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
5	E2F6	chr4:77171918-77173496	H1-hESC	embryonic stem cell:	n/a	chr4:77172784-77172794 chr4:77172837-77172847 chr4:77173336-77173346 chr4:77173185-77173194
6	GATA2	chr4:77172305-77173537	SH-SY5Y	brain:	n/a	n/a
7	SIN3AK20	chr4:77172141-77173631	MCF-7	breast:	n/a	n/a
8	YY1	chr4:77172570-77173491	H1-hESC	embryonic stem cell:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
9	RFX5	chr4:77171716-77173784	SK-N-SH	brain:	n/a	chr4:77172778-77172794 chr4:77172825-77172839 chr4:77172823-77172837 chr4:77172827-77172836 chr4:77172780-77172789

No.	Distal block	Cell Line	Cell type
1	chr4:77154984..77156976-chr4:77172946..77174616,2	K562	blood:
2	chr4:77133278..77135557-chr4:77171656..77174471,3	MCF-7	breast:
3	chr4:77171208..77175531-chr4:77176138..77180024,6	K562	blood:
4	chr4:77171768..77173922-chr4:77226650..77228948,4	MCF-7	breast:

Variant related genes	Relation type
FAM47E	TF binding region
ENSG00000189157	Chromatin interaction
ENSG00000138760	Chromatin interaction
ENSG00000118804	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1036787	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10446680	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097296	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11737624	0.88[ASN][1000 genomes]
rs12331583	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12501795	0.88[ASN][1000 genomes]
rs1348206	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1348208	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372408	0.88[ASN][1000 genomes]
rs1441906	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1441907	0.88[ASN][1000 genomes]
rs1441908	0.89[ASN][1000 genomes]
rs1441917	0.88[ASN][1000 genomes]
rs1441918	0.88[ASN][1000 genomes]
rs1441919	0.88[ASN][1000 genomes]
rs1441921	0.88[ASN][1000 genomes]
rs1441922	0.88[ASN][1000 genomes]
rs2197102	0.88[ASN][1000 genomes]
rs2218264	0.88[ASN][1000 genomes]
rs28530675	0.84[ASN][1000 genomes]
rs28592037	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28718095	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2904215	0.88[ASN][1000 genomes]
rs2904216	0.88[ASN][1000 genomes]
rs35177915	0.88[ASN][1000 genomes]
rs35851125	0.88[ASN][1000 genomes]
rs3919711	0.88[ASN][1000 genomes]
rs4859645	0.83[ASN][1000 genomes]
rs4859647	0.91[ASN][1000 genomes]
rs6532316	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6814385	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6837231	0.85[ASN][1000 genomes]
rs6837841	0.88[ASN][1000 genomes]
rs6854218	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7657929	0.89[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	esv2760851	chr4:77164549-77185144	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv516357	chr4:77167242-77178379	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2421530	chr4:77167242-77178676	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77171600-77173800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:77172000-77173600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:77172000-77173600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr4:77172200-77173600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:77172200-77173600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:77172200-77173600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
7	chr4:77172200-77173600	Active TSS	Right Atrium	heart
8	chr4:77172200-77173600	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr4:77172200-77173800	Active TSS	Brain Anterior Caudate	brain
10	chr4:77172400-77173600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:77172400-77173600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr4:77172400-77173600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:77172400-77173600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr4:77172400-77173600	Active TSS	Left Ventricle	heart
15	chr4:77172400-77173600	Bivalent/Poised TSS	HSMM	muscle
16	chr4:77172400-77173800	Active TSS	Fetal Brain Male	brain
17	chr4:77172600-77173600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr4:77172600-77173600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr4:77172600-77173600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:77172600-77173600	Active TSS	Brain Hippocampus Middle	brain
21	chr4:77172600-77173600	Active TSS	Fetal Heart	heart
22	chr4:77172600-77173600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr4:77172600-77173600	Active TSS	Rectal Smooth Muscle	rectum
24	chr4:77172600-77173600	Bivalent/Poised TSS	Osteobl	bone
25	chr4:77172600-77173800	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr4:77172600-77174000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:77172800-77173600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr4:77172800-77173600	Active TSS	Fetal Brain Female	brain
29	chr4:77173000-77173600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
30	chr4:77173000-77173600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr4:77173000-77173600	Flanking Active TSS	Pancreas	Pancrea
32	chr4:77173000-77173800	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr4:77173200-77173600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:77173200-77173600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:77173200-77173600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
36	chr4:77173200-77173600	Flanking Active TSS	Stomach Mucosa	stomach
37	chr4:77173200-77173800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:77173200-77173800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:77173200-77173800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:77173400-77173600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
41	chr4:77173400-77173600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
42	chr4:77173400-77173600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:77173400-77173600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr4:77173400-77173600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:77173400-77173600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:77173400-77173600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
47	chr4:77173400-77173600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:77173400-77173600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:77173400-77173600	Enhancers	Liver	Liver
50	chr4:77173400-77173600	Bivalent Enhancer	Brain Germinal Matrix	brain

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