Variant report

Variant	rs558907350
Chromosome Location	chr1:61547770-61547771
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	MAX	chr1:61547226-61547927	ECC-1	luminal epithelium:	n/a	chr1:61547871-61547881
2	JUND	chr1:61547274-61548337	K562	blood:	n/a	chr1:61547876-61547885 chr1:61547374-61547383 chr1:61547880-61547889
3	EP300	chr1:61547646-61547878	HepG2	liver:	n/a	chr1:61547774-61547784 chr1:61547734-61547750
4	CHD2	chr1:61547112-61547938	HepG2	liver:	n/a	n/a
5	ZKSCAN1	chr1:61547571-61547815	Hela-S3	cervix:	n/a	n/a
6	MAX	chr1:61547005-61549445	A549	lung:	n/a	chr1:61548660-61548670 chr1:61548738-61548747 chr1:61548820-61548835 chr1:61548826-61548833 chr1:61547871-61547881
7	TBP	chr1:61547205-61549605	K562	blood:	n/a	n/a
8	RCOR1	chr1:61546747-61548442	K562	blood:	n/a	n/a
9	POLR2A	chr1:61547602-61549051	HepG2	liver:	n/a	n/a
10	SMC3	chr1:61547639-61547771	K562	blood:	n/a	n/a
11	HEY1	chr1:61547517-61547845	HepG2	liver:	n/a	n/a
12	TCF12	chr1:61547228-61548002	A549	lung:	n/a	chr1:61547774-61547783
13	HMGN3	chr1:61547490-61548469	K562	blood:	n/a	n/a
14	CEBPB	chr1:61547632-61547794	HepG2	liver:	n/a	n/a
15	FOXA2	chr1:61547417-61548084	A549	lung:	n/a	chr1:61547771-61547783
16	POLR2A	chr1:61547538-61548519	ECC-1	luminal epithelium:	n/a	n/a
17	E2F4	chr1:61547602-61548456	K562	blood:	n/a	chr1:61548154-61548165 chr1:61547873-61547882 chr1:61548019-61548029
18	FOXA2	chr1:61547610-61547945	HepG2	liver:	n/a	chr1:61547771-61547783
19	POLR2A	chr1:61547610-61547931	HCT-116	colon:	n/a	n/a
20	MYC	chr1:61547753-61547860	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:61547685-61549673	Hela-S3	cervix:	n/a	n/a
22	YY1	chr1:61547755-61548388	K562	blood:	n/a	chr1:61547978-61547989 chr1:61547876-61547885 chr1:61547873-61547882 chr1:61547874-61547885 chr1:61548015-61548026
23	ZMIZ1	chr1:61547075-61547844	K562	blood:	n/a	n/a
24	POLR2A	chr1:61547467-61548815	K562	blood:	n/a	n/a
25	POLR2A	chr1:61547681-61547856	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:61547176-61549379	MCF10A-Er-Src	breast:	n/a	n/a
27	SP1	chr1:61547375-61548494	A549	lung:	n/a	chr1:61547739-61547749 chr1:61547869-61547883 chr1:61547873-61547882 chr1:61547742-61547756 chr1:61548040-61548054 chr1:61548027-61548036 chr1:61547874-61547883 chr1:61547873-61547883 chr1:61548039-61548051 chr1:61547867-61547876 chr1:61547739-61547748 chr1:61548025-61548037 chr1:61548026-61548040 chr1:61548034-61548044 chr1:61547866-61547878 chr1:61548041-61548050 chr1:61547872-61547884 chr1:61548025-61548037 chr1:61547866-61547878 chr1:61547872-61547884 chr1:61548039-61548051
28	FOXA1	chr1:61547616-61547874	T-47D	breast:	n/a	chr1:61547771-61547783
29	POLR2A	chr1:61547280-61547844	PANC-1	pancreas:	n/a	n/a
30	ZBTB7A	chr1:61547068-61548004	ECC-1	luminal epithelium:	n/a	chr1:61547375-61547389
31	CTCF	chr1:61547640-61547790	HMEC	breast:	n/a	n/a
32	EP300	chr1:61547518-61547998	HepG2	liver:	n/a	chr1:61547774-61547784 chr1:61547734-61547750
33	RAD21	chr1:61547589-61547900	HepG2	liver:	n/a	n/a
34	CEBPB	chr1:61547568-61547900	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:61547126-61549706	Hela-S3	cervix:	n/a	n/a
36	HEY1	chr1:61547415-61548502	HepG2	liver:	n/a	chr1:61548014-61548029 chr1:61547975-61547990 chr1:61548011-61548026 chr1:61547874-61547889
37	SIN3A	chr1:61547341-61547871	H1-hESC	embryonic stem cell:	n/a	n/a
38	HEY1	chr1:61547664-61548413	K562	blood:	n/a	chr1:61548014-61548029 chr1:61547975-61547990 chr1:61548011-61548026 chr1:61547874-61547889
39	EGR1	chr1:61547293-61548485	K562	blood:	n/a	chr1:61547876-61547886 chr1:61548022-61548032 chr1:61547734-61547747 chr1:61547420-61547429 chr1:61548022-61548035 chr1:61548023-61548033 chr1:61547868-61547881 chr1:61548021-61548036 chr1:61547867-61547882 chr1:61548028-61548041 chr1:61548035-61548050 chr1:61547868-61547881 chr1:61547373-61547383 chr1:61547870-61547880 chr1:61547419-61547432 chr1:61547737-61547746 chr1:61547372-61547382 chr1:61547734-61547747 chr1:61547873-61547883 chr1:61548022-61548035
40	FOXA1	chr1:61547471-61548011	HepG2	liver:	n/a	chr1:61547771-61547783
41	POLR2A	chr1:61547481-61549674	K562	blood:	n/a	n/a
42	NR3C1	chr1:61547648-61547948	ECC-1	luminal epithelium:	n/a	chr1:61547781-61547802
43	RAD21	chr1:61547367-61547960	SK-N-SH_RA	brain:	n/a	n/a
44	MAX	chr1:61547624-61547832	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:61547551-61548786	HEK293	kidney:	n/a	n/a
46	SMARCB1	chr1:61547227-61549647	Hela-S3	cervix:	n/a	n/a
47	MAX	chr1:61547459-61549054	HepG2	liver:	n/a	chr1:61548660-61548670 chr1:61548738-61548747 chr1:61548820-61548835 chr1:61548826-61548833 chr1:61547871-61547881
48	NR3C1	chr1:61547440-61548003	A549	lung:	n/a	chr1:61547781-61547802
49	TCF7L2	chr1:61547346-61548486	HCT-116	colon:	n/a	n/a
50	REST	chr1:61547477-61547878	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:61547758-61547808	Hepatocyte	liver:	n/a
2	chr1:61547758-61547808	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:61547758-61547808	PANC-1	pancreas:	n/a
4	chr1:61547758-61547808	PrEC	prostate:	n/a
5	chr1:61547758-61547808	SK-N-MC	brain:	n/a
6	chr1:61547758-61547808	ovcar-3	ovarian:	n/a
7	chr1:61547758-61547808	LNCaP	prostate:	n/a
8	chr1:61547758-61547808	HRPEpiC	eye:	n/a
9	chr1:61547758-61547808	NH-A	brain:	n/a
10	chr1:61547758-61547808	HUVEC	blood vessel:	n/a
11	chr1:61547758-61547808	ProgFib	skin:	n/a
12	chr1:61547758-61547808	HEEpiC	esophagus:	n/a
13	chr1:61547758-61547808	GM12892	blood:	n/a
14	chr1:61547758-61547808	K562	blood:	n/a
15	chr1:61547758-61547808	GM12891	blood:	n/a
16	chr1:61547758-61547808	HCT-116	colon:	n/a
17	chr1:61547758-61547808	AoSMC	blood vessel:	n/a
18	chr1:61547758-61547808	BE2_C	brain:	n/a
19	chr1:61547758-61547808	NT2-D1	testis:	n/a
20	chr1:61547758-61547808	AG09319	gingival:	n/a
21	chr1:61547758-61547808	GM12878	blood:	n/a
22	chr1:61547758-61547808	SK-N-SH_RA	brain:	n/a
23	chr1:61547758-61547808	HCPEpiC	choroid plexus:	n/a
24	chr1:61547758-61547808	AG10803	skin:	n/a
25	chr1:61547758-61547808	NB4	blood:	n/a
26	chr1:61547758-61547808	HCM	heart:	n/a
27	chr1:61547758-61547808	SKMC	muscle:	n/a
28	chr1:61547758-61547808	PFSK-1	brain:	n/a
29	chr1:61547758-61547808	SAEC	small airway:	n/a
30	chr1:61547758-61547808	SK-N-SH	brain:	n/a
31	chr1:61547758-61547808	NHDF-neo	bronchial:	n/a
32	chr1:61547758-61547808	U87	brain:	n/a
33	chr1:61547758-61547808	HepG2	liver:	n/a
34	chr1:61547758-61547808	BJ	skin:	n/a
35	chr1:61547758-61547808	AG04450	lung:	fetal
36	chr1:61547758-61547808	RPTEC	kidney:	n/a
37	chr1:61547758-61547808	HRE	kidney:	n/a
38	chr1:61547758-61547808	AG09309	skin:	n/a
39	chr1:61547758-61547808	HAEpiC	amniotic membrane:	n/a
40	chr1:61547758-61547808	MCF-7	breast:	n/a
41	chr1:61547758-61547808	GM19239	blood:	n/a
42	chr1:61547758-61547808	T-47D	breast:	n/a
43	chr1:61547758-61547808	HEK293	kidney:	embryo
44	chr1:61547758-61547808	HMEC	breast:	n/a
45	chr1:61547758-61547808	HL-60	blood:	n/a
46	chr1:61547758-61547808	ECC-1	luminal epithelium:	n/a
47	chr1:61547758-61547808	NHBE	bronchial:	n/a
48	chr1:61547758-61547808	AG04449	skin:	fetal
49	chr1:61547758-61547808	HIPEpiC	eye:	n/a
50	chr1:61547758-61547808	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:61513320..61528030-chr1:61539604..61553659,57	K562	blood:
2	chr1:61541387..61547328-chr1:61547444..61551394,9	MCF-7	breast:
3	chr1:61546491..61548608-chr1:61718284..61720951,3	K562	blood:
4	chr1:61512478..61530748-chr1:61539371..61553659,68	K562	blood:

Variant related genes	Relation type
NFIA	TF binding region
NFIA	CpG island
ENSG00000162599	Chromatin interaction
ENSG00000237853	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3366378	chr1:61547039-61549112	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	esv19873	chr1:61547702-61549738	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv546369	chr1:61547731-61549300	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv546370	chr1:61547731-61549494	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61545200-61547800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:61545200-61547800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:61545600-61550600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr1:61545600-61552000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr1:61545600-61553800	Active TSS	Aorta	Aorta
6	chr1:61545800-61550600	Active TSS	Fetal Muscle Trunk	muscle
7	chr1:61545800-61550600	Active TSS	Right Ventricle	heart
8	chr1:61546200-61547800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr1:61546600-61547800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr1:61546800-61547800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr1:61546800-61549800	Active TSS	Brain Cingulate Gyrus	brain
12	chr1:61546800-61550600	Active TSS	Colonic Mucosa	Colon
13	chr1:61547000-61547800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:61547000-61547800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:61547000-61547800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
16	chr1:61547000-61549600	Active TSS	Brain Anterior Caudate	brain
17	chr1:61547000-61549800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr1:61547000-61549800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:61547000-61549800	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr1:61547000-61550200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:61547000-61550200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:61547000-61550400	Active TSS	Brain Angular Gyrus	brain
23	chr1:61547000-61550400	Active TSS	HSMMtube	muscle
24	chr1:61547000-61550600	Active TSS	Left Ventricle	heart
25	chr1:61547000-61550600	Active TSS	Ovary	ovary
26	chr1:61547000-61552000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:61547000-61552000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:61547000-61554200	Active TSS	Right Atrium	heart
29	chr1:61547200-61547800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:61547200-61547800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:61547200-61547800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr1:61547200-61547800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr1:61547200-61547800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:61547200-61548200	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr1:61547200-61549600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:61547200-61549800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:61547200-61549800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:61547200-61549800	Active TSS	Pancreas	Pancrea
39	chr1:61547200-61550000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr1:61547200-61550200	Active TSS	Small Intestine	intestine
41	chr1:61547200-61550200	Bivalent/Poised TSS	HepG2	liver
42	chr1:61547200-61550200	Active TSS	NHDF-Ad	bronchial
43	chr1:61547200-61550400	Active TSS	Brain Substantia Nigra	brain
44	chr1:61547200-61550400	Active TSS	Esophagus	oesophagus
45	chr1:61547200-61550400	Active TSS	A549	lung
46	chr1:61547200-61550600	Active TSS	Colon Smooth Muscle	Colon
47	chr1:61547200-61550800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:61547200-61551400	Active TSS	Brain Hippocampus Middle	brain
49	chr1:61547200-61552000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:61547200-61552200	Active TSS	Rectal Smooth Muscle	rectum

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