Variant report

Variant	rs6824124
Chromosome Location	chr4:55991779-55991780
allele	A/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	TAF1	chr4:55991511-55992040	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:55991541-55992015	U87	brain:	n/a	n/a
3	POLR2A	chr4:55991547-55992015	U87	brain:	n/a	n/a
4	POLR2A	chr4:55991424-55992034	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr4:55989980-55992078	HUVEC	blood vessel:	n/a	n/a
6	ZBTB7A	chr4:55991465-55992024	ECC-1	luminal epithelium:	n/a	chr4:55991719-55991730
7	MYC	chr4:55991645-55991828	H1-hESC	embryonic stem cell:	n/a	chr4:55991807-55991816
8	POLR2A	chr4:55991608-55991808	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr4:55991541-55992060	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3AK20	chr4:55991340-55991779	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr4:55989465-55992006	HUVEC	blood vessel:	n/a	n/a
12	RAD21	chr4:55990843-55992293	H1-hESC	embryonic stem cell:	n/a	n/a
13	NFIC	chr4:55991356-55991830	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr4:55991546-55991820	ECC-1	luminal epithelium:	n/a	n/a
15	SIN3A	chr4:55989949-55992606	H1-hESC	embryonic stem cell:	n/a	chr4:55992582-55992596 chr4:55990281-55990291 chr4:55990226-55990236 chr4:55991604-55991617
16	POLR2A	chr4:55991577-55991961	H1-hESC	embryonic stem cell:	n/a	n/a
17	TAF7	chr4:55991449-55991913	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr4:55991402-55992319	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZBTB7A	chr4:55991502-55991996	ECC-1	luminal epithelium:	n/a	chr4:55991719-55991730
20	POLR2A	chr4:55991404-55992150	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr4:55991329-55992056	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr4:55991776-55992289	K562	blood:	n/a	n/a
23	CTBP2	chr4:55991292-55992711	H1-hESC	embryonic stem cell:	n/a	n/a
24	TBP	chr4:55991423-55992220	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:55991296-55992073	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr4:55991176-55992455	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr4:55991423-55991981	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr4:55991548-55991907	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDR-3	chr4:55988831-55992348	ucscGeneNc_uc003hay_2

Variant related genes	Relation type
KDR	TF binding region

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10011355	1.00[AMR][1000 genomes]
rs10027862	1.00[AMR][1000 genomes]
rs12716019	1.00[AMR][1000 genomes]
rs1380065	1.00[AMR][1000 genomes]
rs1380070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1458821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1543930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1543931	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1551639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1870380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1968771	1.00[AMR][1000 genomes]
rs2168946	1.00[AMR][1000 genomes]
rs2412636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4352535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57190330	1.00[AMR][1000 genomes]
rs59384774	1.00[AMR][1000 genomes]
rs60067051	1.00[AMR][1000 genomes]
rs6554250	1.00[AMR][1000 genomes]
rs6826761	1.00[AMR][1000 genomes]
rs6835605	1.00[AMR][1000 genomes]
rs6855258	1.00[AMR][1000 genomes]
rs6857669	1.00[AMR][1000 genomes]
rs73816854	1.00[AMR][1000 genomes]
rs73816855	1.00[AMR][1000 genomes]
rs73816856	1.00[AMR][1000 genomes]
rs7666097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv829939	chr4:55856771-56005011	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 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	chr4:55988000-55992400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:55988000-55992400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:55988600-55992600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr4:55989400-55992400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr4:55989800-55992200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
6	chr4:55989800-55992800	Bivalent/Poised TSS	Fetal Kidney	kidney
7	chr4:55990000-55992400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr4:55990000-55992400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:55990000-55992400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:55990200-55992400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:55990200-55992400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
12	chr4:55990200-55992600	Bivalent/Poised TSS	Ovary	ovary
13	chr4:55990400-55991800	Bivalent/Poised TSS	Liver	Liver
14	chr4:55990400-55992200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
15	chr4:55990400-55992400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr4:55990400-55992400	Bivalent/Poised TSS	Left Ventricle	heart
17	chr4:55990600-55991800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:55990600-55992200	Active TSS	Brain Cingulate Gyrus	brain
19	chr4:55990600-55992200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
20	chr4:55990600-55992400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
21	chr4:55990600-55992400	Active TSS	Brain Substantia Nigra	brain
22	chr4:55990600-55992400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
23	chr4:55990600-55992600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr4:55990600-55992600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:55990600-55992600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:55990800-55991800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
27	chr4:55990800-55992000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr4:55990800-55992000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:55990800-55992200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:55990800-55992400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr4:55990800-55992400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
32	chr4:55990800-55992400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr4:55990800-55992600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr4:55991000-55991800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
35	chr4:55991000-55992000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:55991000-55992000	Bivalent/Poised TSS	Colonic Mucosa	Colon
37	chr4:55991000-55992000	Active TSS	HUVEC	blood vessel
38	chr4:55991000-55992200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:55991000-55992200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
40	chr4:55991000-55992200	Flanking Bivalent TSS/Enh	Placenta	Placenta
41	chr4:55991000-55992400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:55991000-55992400	Active TSS	Aorta	Aorta
43	chr4:55991000-55992600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:55991000-55992600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
45	chr4:55991200-55991800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:55991200-55991800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:55991200-55991800	Flanking Active TSS	Spleen	Spleen
48	chr4:55991200-55992200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:55991200-55992200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:55991200-55992200	Active TSS	Gastric	stomach

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