Variant report

Variant	rs554997222
Chromosome Location	chr4:95678894-95678895
allele	C/G
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	POLR2A	chr4:95678892-95679260	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr4:95678875-95679031	Medullo	brain:	n/a	n/a
3	CTCF	chr4:95678880-95679030	MCF-7	breast:	n/a	n/a
4	CTCF	chr4:95678860-95679010	HUVEC	blood vessel:	n/a	n/a
5	MXI1	chr4:95677488-95681982	SK-N-SH	brain:	n/a	chr4:95679721-95679730
6	POLR2A	chr4:95678765-95678985	MCF-7	breast:	n/a	n/a
7	MAX	chr4:95678600-95680454	A549	lung:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
8	POLR2A	chr4:95678612-95679216	PFSK-1	brain:	n/a	n/a
9	RAD21	chr4:95678727-95679089	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr4:95678575-95680180	IMR90	lung:	n/a	chr4:95679721-95679730
11	CTCF	chr4:95678850-95679013	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr4:95678820-95678970	HUVEC	blood vessel:	n/a	n/a
13	CTCF	chr4:95678840-95678990	NHEK	skin:	n/a	n/a
14	CTCF	chr4:95678860-95679010	AoAF	blood vessel:	n/a	n/a
15	POLR2A	chr4:95678469-95679094	PFSK-1	brain:	n/a	n/a
16	CTCF	chr4:95678880-95679030	HPAF	blood vessel:	n/a	n/a
17	HA-E2F1	chr4:95678701-95680381	MCF-7	breast:	n/a	chr4:95679542-95679552 chr4:95679544-95679553 chr4:95680197-95680204 chr4:95679618-95679630 chr4:95679539-95679549
18	POLR2A	chr4:95678205-95680130	MCF10A-Er-Src	breast:	n/a	n/a
19	RAD21	chr4:95678727-95679112	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr4:95678860-95679010	A549	lung:	n/a	n/a
21	CTCF	chr4:95678861-95678993	MCF-7	breast:	n/a	n/a
22	NFIC	chr4:95678759-95679118	ECC-1	luminal epithelium:	n/a	n/a
23	RAD21	chr4:95677342-95679343	SK-N-SH	brain:	n/a	n/a
24	EP300	chr4:95678767-95679081	SK-N-SH_RA	brain:	n/a	chr4:95678846-95678862
25	POLR2A	chr4:95678565-95679131	H1-neurons	neurons:	n/a	n/a
26	FOS	chr4:95678733-95678990	HUVEC	blood vessel:	n/a	n/a
27	YY1	chr4:95678765-95679036	A549	lung:	n/a	chr4:95678870-95678884 chr4:95678890-95678899
28	CTBP2	chr4:95678812-95680327	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr4:95678623-95679171	ECC-1	luminal epithelium:	n/a	n/a
30	CTCF	chr4:95678860-95679010	HMF	breast:	n/a	n/a
31	CREB1	chr4:95678728-95679047	A549	lung:	n/a	n/a
32	TAF1	chr4:95678751-95678991	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr4:95678820-95678970	BJ	skin:	n/a	n/a
34	RAD21	chr4:95678717-95679484	IMR90	lung:	n/a	n/a
35	POLR2A	chr4:95678719-95680358	A549	lung:	n/a	n/a
36	CTCF	chr4:95678860-95679010	HRE	kidney:	n/a	n/a
37	CTCF	chr4:95678820-95678970	AG09319	gingival:	n/a	n/a
38	CHD2	chr4:95678813-95679126	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr4:95678828-95679924	HEK293	kidney:	n/a	n/a
40	CTCF	chr4:95678880-95679030	HEEpiC	esophagus:	n/a	n/a
41	CTCF	chr4:95678840-95678990	HVMF	connective:	n/a	n/a
42	TAF1	chr4:95678798-95679739	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr4:95678728-95679877	ECC-1	luminal epithelium:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
44	CTCF	chr4:95678885-95678981	MCF-7	breast:	n/a	n/a
45	CTCF	chr4:95678880-95679030	AG10803	skin:	n/a	n/a
46	CTCF	chr4:95678872-95678993	NHEK	skin:	n/a	n/a
47	CHD1	chr4:95677993-95680028	IMR90	lung:	n/a	chr4:95679126-95679136 chr4:95679131-95679141
48	TAF1	chr4:95678712-95679106	PFSK-1	brain:	n/a	n/a
49	CTCF	chr4:95678860-95679010	HA-sp	spinal cord:	n/a	n/a
50	POLR2A	chr4:95678754-95678952	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95675993..95678993-chr6:26054520..26056880,3	K562	blood:
2	chr4:95678678..95680883-chr4:96023985..96026151,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UNC5C-1	chr4:95678545-95679011	XLOC_004019
2	lnc-UNC5C-1	chr4:95678545-95679036	NONHSAT097457

Variant related genes	Relation type
ENSG00000249599	TF binding region
BMPR1B	TF binding region
ENSG00000187837	Chromatin interaction
ENSG00000138696	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv1833916	chr4:95673181-95679741	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3407255	chr4:95677954-95680802	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95677800-95681800	Active TSS	A549	lung
2	chr4:95678000-95679000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
3	chr4:95678000-95680000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:95678000-95680200	Active TSS	NH-A	brain
5	chr4:95678000-95682000	Active TSS	Stomach Smooth Muscle	stomach
6	chr4:95678200-95679000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:95678200-95679000	Flanking Bivalent TSS/Enh	Dnd41	blood
8	chr4:95678200-95679600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
9	chr4:95678200-95680000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:95678200-95680400	Active TSS	Aorta	Aorta
11	chr4:95678200-95680400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
12	chr4:95678200-95680400	Active TSS	HMEC	breast
13	chr4:95678400-95679000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:95678400-95679400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:95678400-95679600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:95678400-95679600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:95678400-95679600	Active TSS	Fetal Brain Female	brain
18	chr4:95678400-95679800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:95678400-95679800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:95678400-95680000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:95678400-95680000	Bivalent/Poised TSS	Thymus	Thymus
22	chr4:95678400-95680200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:95678400-95680200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:95678400-95680400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr4:95678400-95680600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr4:95678400-95680600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr4:95678400-95680600	Active TSS	Ovary	ovary
28	chr4:95678400-95680800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:95678400-95680800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:95678600-95679000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
32	chr4:95678600-95679000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:95678600-95679000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr4:95678600-95679000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
35	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:95678600-95679000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
39	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
40	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr4:95678600-95679000	Bivalent Enhancer	Fetal Heart	heart
42	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr4:95678600-95679000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
44	chr4:95678600-95679000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
45	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
46	chr4:95678600-95679000	Flanking Active TSS	HSMM	muscle
47	chr4:95678600-95679000	Bivalent/Poised TSS	NHDF-Ad	bronchial
48	chr4:95678600-95679000	Flanking Active TSS	NHEK	skin
49	chr4:95678600-95679000	Flanking Bivalent TSS/Enh	Osteobl	bone
50	chr4:95678600-95679200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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