Variant report

Variant	rs4859647
Chromosome Location	chr4:77173299-77173300
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	YY1	chr4:77172704-77173470	SK-N-SH_RA	brain:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
2	SIN3A	chr4:77172539-77173394	H1-hESC	embryonic stem cell:	n/a	chr4:77172983-77172992 chr4:77172716-77172729
3	POLR2A	chr4:77172426-77173313	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr4:77173220-77173370	HCFaa	heart:	n/a	n/a
5	YY1	chr4:77172646-77173404	SK-N-SH	brain:	n/a	chr4:77173051-77173060 chr4:77173049-77173060
6	EP300	chr4:77173213-77173483	SK-N-SH_RA	brain:	n/a	n/a
7	EP300	chr4:77173066-77173517	SK-N-SH_RA	brain:	n/a	n/a
8	YY1	chr4:77172657-77173435	SK-N-SH_RA	brain:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
9	POLR2A	chr4:77172563-77173303	MCF-7	breast:	n/a	n/a
10	ZNF143	chr4:77172475-77173424	H1-hESC	embryonic stem cell:	n/a	chr4:77173184-77173202
11	YY1	chr4:77172536-77173497	H1-hESC	embryonic stem cell:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
12	E2F6	chr4:77171918-77173496	H1-hESC	embryonic stem cell:	n/a	chr4:77172784-77172794 chr4:77172837-77172847 chr4:77173336-77173346 chr4:77173185-77173194
13	RAD21	chr4:77172584-77173329	MCF-7	breast:	n/a	n/a
14	ZBTB7A	chr4:77172727-77173364	ECC-1	luminal epithelium:	n/a	n/a
15	YY1	chr4:77172622-77173449	SK-N-SH	brain:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
16	RAD21	chr4:77172611-77173363	SK-N-SH_RA	brain:	n/a	n/a
17	RAD21	chr4:77172825-77173305	SK-N-SH_RA	brain:	n/a	n/a
18	GATA2	chr4:77172305-77173537	SH-SY5Y	brain:	n/a	n/a
19	SIN3AK20	chr4:77172141-77173631	MCF-7	breast:	n/a	n/a
20	TAF1	chr4:77172709-77173351	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr4:77172570-77173491	H1-hESC	embryonic stem cell:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
22	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
ENSG00000118804	Chromatin interaction
ENSG00000189157	Chromatin interaction
ENSG00000138760	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10446680	0.87[ASN][1000 genomes]
rs11097296	0.84[ASN][1000 genomes]
rs11097297	0.85[ASN][1000 genomes]
rs11737624	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12331583	0.84[ASN][1000 genomes]
rs12501795	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1348206	0.87[ASN][1000 genomes]
rs1348208	0.87[ASN][1000 genomes]
rs1372408	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441906	0.87[ASN][1000 genomes]
rs1441907	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441908	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1441917	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441918	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441919	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441921	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441922	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2197102	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2218264	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28530675	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28718095	0.90[ASN][1000 genomes]
rs2904215	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2904216	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35177915	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35851125	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3919711	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859645	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56371028	0.91[ASN][1000 genomes]
rs6814385	0.84[ASN][1000 genomes]
rs6837231	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6837841	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854218	0.84[ASN][1000 genomes]
rs6855568	0.84[ASN][1000 genomes]
rs7657929	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77171600-77173800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:77172000-77173400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:77172000-77173600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:77172000-77173600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr4:77172200-77173400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr4:77172200-77173400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:77172200-77173400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr4:77172200-77173400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr4:77172200-77173400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr4:77172200-77173400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr4:77172200-77173400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:77172200-77173400	Flanking Active TSS	Liver	Liver
13	chr4:77172200-77173400	Active TSS	Colonic Mucosa	Colon
14	chr4:77172200-77173400	Active TSS	Colon Smooth Muscle	Colon
15	chr4:77172200-77173400	Active TSS	Right Ventricle	heart
16	chr4:77172200-77173400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
17	chr4:77172200-77173400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr4:77172200-77173600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr4:77172200-77173600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:77172200-77173600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr4:77172200-77173600	Active TSS	Right Atrium	heart
22	chr4:77172200-77173600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr4:77172200-77173800	Active TSS	Brain Anterior Caudate	brain
24	chr4:77172400-77173400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:77172400-77173400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:77172400-77173400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:77172400-77173400	Active TSS	Aorta	Aorta
28	chr4:77172400-77173400	Active TSS	Brain Cingulate Gyrus	brain
29	chr4:77172400-77173400	Active TSS	Brain Substantia Nigra	brain
30	chr4:77172400-77173400	Active TSS	Gastric	stomach
31	chr4:77172400-77173400	Bivalent/Poised TSS	HSMMtube	muscle
32	chr4:77172400-77173600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr4:77172400-77173600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr4:77172400-77173600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr4:77172400-77173600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr4:77172400-77173600	Active TSS	Left Ventricle	heart
37	chr4:77172400-77173600	Bivalent/Poised TSS	HSMM	muscle
38	chr4:77172400-77173800	Active TSS	Fetal Brain Male	brain
39	chr4:77172600-77173400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
40	chr4:77172600-77173400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr4:77172600-77173400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:77172600-77173400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:77172600-77173400	Active TSS	Brain Angular Gyrus	brain
44	chr4:77172600-77173400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
45	chr4:77172600-77173400	Active TSS	Duodenum Mucosa	Duodenum
46	chr4:77172600-77173400	Bivalent/Poised TSS	Fetal Kidney	kidney
47	chr4:77172600-77173400	Bivalent/Poised TSS	Fetal Lung	lung
48	chr4:77172600-77173400	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr4:77172600-77173600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr4:77172600-77173600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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