Variant report

Variant	rs564504046
Chromosome Location	chr4:47916088-47916089
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:232)
CpG islands
(count:122)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:232 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:47915779-47917050	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr4:47916020-47916170	GM12864	blood:	n/a	n/a
3	POLR2A	chr4:47915786-47917044	GM18526	blood:	n/a	n/a
4	POLR2A	chr4:47915775-47916141	Hela-S3	cervix:	n/a	n/a
5	RELA	chr4:47915447-47917043	GM15510	blood:	n/a	n/a
6	POLR2A	chr4:47915664-47917000	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:47915741-47917060	Hela-S3	cervix:	n/a	n/a
8	SIN3AK20	chr4:47915690-47917128	MCF-7	breast:	n/a	n/a
9	ZEB1	chr4:47915710-47917010	GM12878	blood:	n/a	chr4:47915954-47915961 chr4:47916921-47916933 chr4:47916923-47916930
10	POLR2A	chr4:47915723-47916962	MCF-7	breast:	n/a	n/a
11	POLR2A	chr4:47915516-47917078	NB4	blood:	n/a	n/a
12	POLR2A	chr4:47915898-47916966	Gliobla	brain:	n/a	n/a
13	CTCF	chr4:47916060-47916210	SAEC	small airway:	n/a	n/a
14	ETS1	chr4:47915867-47917087	GM12878	blood:	n/a	chr4:47916789-47916802 chr4:47916793-47916800 chr4:47916788-47916801
15	POLR2A	chr4:47915958-47916747	HepG2	liver:	n/a	n/a
16	ZBTB7A	chr4:47915823-47917124	ECC-1	luminal epithelium:	n/a	n/a
17	RUNX3	chr4:47915767-47916155	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:47915807-47916761	IMR90	lung:	n/a	n/a
19	POLR2A	chr4:47915717-47916948	MCF-7	breast:	n/a	n/a
20	MAX	chr4:47915367-47917156	Hela-S3	cervix:	n/a	n/a
21	ELF1	chr4:47915759-47916931	GM12878	blood:	n/a	chr4:47915913-47915922
22	POLR2A	chr4:47915370-47917105	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:47916078-47917004	PFSK-1	brain:	n/a	n/a
24	CTCF	chr4:47916074-47916139	GM10248	blood:	n/a	n/a
25	CTCF	chr4:47916040-47916190	GM12865	blood:	n/a	n/a
26	YY1	chr4:47915766-47916251	SK-N-SH_RA	brain:	n/a	chr4:47915913-47915922 chr4:47916135-47916152
27	CTCF	chr4:47916060-47916210	SK-N-SH_RA	brain:	n/a	n/a
28	POLR2A	chr4:47915699-47916867	GM12892	blood:	n/a	n/a
29	MXI1	chr4:47915452-47917184	HepG2	liver:	n/a	n/a
30	POLR2A	chr4:47915315-47917247	GM12891	blood:	n/a	n/a
31	POLR2A	chr4:47915823-47916197	HCT-116	colon:	n/a	n/a
32	CTCF	chr4:47916060-47916210	GM06990	blood:	n/a	n/a
33	MYC	chr4:47915777-47916962	MCF-7	breast:	n/a	n/a
34	BACH1	chr4:47915971-47917059	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr4:47915344-47917165	K562	blood:	n/a	n/a
36	CTCF	chr4:47916080-47916230	K562	blood:	n/a	n/a
37	CTCF	chr4:47916000-47916150	AoAF	blood vessel:	n/a	n/a
38	MAX	chr4:47915655-47917169	HCT-116	colon:	n/a	n/a
39	CTCF	chr4:47916000-47916150	HBMEC	blood vessel:	n/a	n/a
40	CTCF	chr4:47916080-47916230	BJ	skin:	n/a	n/a
41	YY1	chr4:47915772-47917056	ECC-1	luminal epithelium:	n/a	chr4:47915913-47915922 chr4:47916966-47916985 chr4:47916135-47916152 chr4:47916971-47916979
42	YY1	chr4:47915887-47916977	SK-N-SH_RA	brain:	n/a	chr4:47915913-47915922 chr4:47916135-47916152
43	TAF1	chr4:47915742-47916776	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr4:47915794-47917007	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr4:47915842-47916709	A549	lung:	n/a	n/a
46	MXI1	chr4:47915903-47917016	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr4:47915777-47917124	GM12878	blood:	n/a	n/a
48	MAX	chr4:47915718-47917144	A549	lung:	n/a	n/a
49	TAF7	chr4:47915762-47916273	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr4:47915685-47917110	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:47916050-47916100	HMEC	breast:	n/a
2	chr4:47916056-47916106	GM12878	blood:	n/a
3	chr4:47916050-47916100	BE2_C	brain:	n/a
4	chr4:47916050-47916100	IMR90	lung:	fetal
5	chr4:47916050-47916100	HCM	heart:	n/a
6	chr4:47916056-47916106	NHDF-neo	bronchial:	n/a
7	chr4:47916056-47916106	HRCEpiC	kidney:	n/a
8	chr4:47916056-47916106	ProgFib	skin:	n/a
9	chr4:47916056-47916106	NHBE	bronchial:	n/a
10	chr4:47916056-47916106	T-47D	breast:	n/a
11	chr4:47916056-47916106	NH-A	brain:	n/a
12	chr4:47916056-47916106	PFSK-1	brain:	n/a
13	chr4:47916050-47916100	HAEpiC	amniotic membrane:	n/a
14	chr4:47916056-47916106	Jurkat	blood:	n/a
15	chr4:47916056-47916106	Hela-S3	cervix:	n/a
16	chr4:47916056-47916106	CMK	blood:	n/a
17	chr4:47916050-47916100	ECC-1	luminal epithelium:	n/a
18	chr4:47916056-47916106	HRPEpiC	eye:	n/a
19	chr4:47916056-47916106	HMEC	breast:	n/a
20	chr4:47916056-47916106	MCF10A-Er-Src	breast:	n/a
21	chr4:47916056-47916106	AG09309	skin:	n/a
22	chr4:47916056-47916106	SK-N-MC	brain:	n/a
23	chr4:47916056-47916106	HPAEpiC	pulmonary alveolar:	n/a
24	chr4:47916050-47916100	HRPEpiC	eye:	n/a
25	chr4:47916050-47916100	LNCaP	prostate:	n/a
26	chr4:47916056-47916106	HCM	heart:	n/a
27	chr4:47916050-47916100	PANC-1	pancreas:	n/a
28	chr4:47916056-47916106	K562	blood:	n/a
29	chr4:47916056-47916106	SAEC	small airway:	n/a
30	chr4:47916050-47916100	SAEC	small airway:	n/a
31	chr4:47916050-47916100	HL-60	blood:	n/a
32	chr4:47916056-47916106	MCF-7	breast:	n/a
33	chr4:47916056-47916106	BJ	skin:	n/a
34	chr4:47916056-47916106	AG10803	skin:	n/a
35	chr4:47916056-47916106	U87	brain:	n/a
36	chr4:47916056-47916106	Hepatocyte	liver:	n/a
37	chr4:47916050-47916100	GM19239	blood:	n/a
38	chr4:47916050-47916100	SKMC	muscle:	n/a
39	chr4:47916050-47916100	NB4	blood:	n/a
40	chr4:47916056-47916106	NB4	blood:	n/a
41	chr4:47916050-47916100	Hepatocyte	liver:	n/a
42	chr4:47916050-47916100	GM12892	blood:	n/a
43	chr4:47916056-47916106	HUVEC	blood vessel:	n/a
44	chr4:47916050-47916100	HEK293	kidney:	embryo
45	chr4:47916050-47916100	PFSK-1	brain:	n/a
46	chr4:47916056-47916106	HCPEpiC	choroid plexus:	n/a
47	chr4:47916056-47916106	HEEpiC	esophagus:	n/a
48	chr4:47916056-47916106	A549	lung:	n/a
49	chr4:47916056-47916106	HL-60	blood:	n/a
50	chr4:47916056-47916106	LNCaP	prostate:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:47916070..47916645-chr6:32939554..32940093,2	Hela-S3	cervix:
2	chr16:71842665..71843234-chr4:47915439..47916090,2	Hela-S3	cervix:
3	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:
4	chr4:47915045..47916605-chr4:48017433..48018940,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NIPAL1-1	chr4:47915823-47916721	NONHSAT096272

No data

Variant related genes	Relation type
NIPAL1	TF binding region
NIPAL1	CpG island
ENSG00000166747	Chromatin interaction
ENSG00000163293	Chromatin interaction
ENSG00000198515	Chromatin interaction
ENSG00000204256	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	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47913400-47917200	Active TSS	Muscle Satellite Cultured Cells	--
2	chr4:47914200-47917400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:47914400-47917000	Active TSS	GM12878-XiMat	blood
4	chr4:47914400-47917400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:47914400-47917600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:47914400-47917600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr4:47915000-47916800	Active TSS	NHLF	lung
8	chr4:47915000-47917200	Active TSS	HMEC	breast
9	chr4:47915000-47917400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr4:47915000-47917400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr4:47915000-47917400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr4:47915000-47917600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr4:47915200-47916200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr4:47915200-47916200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr4:47915200-47916200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:47915200-47916200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:47915200-47916400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr4:47915200-47916400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:47915200-47917200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:47915200-47917200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr4:47915200-47917200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:47915200-47917200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:47915200-47917200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:47915200-47917200	Active TSS	Aorta	Aorta
25	chr4:47915200-47917200	Active TSS	Pancreas	Pancrea
26	chr4:47915200-47917200	Active TSS	Psoas Muscle	Psoas
27	chr4:47915200-47917400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:47915200-47917400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:47915200-47917400	Active TSS	Brain Germinal Matrix	brain
30	chr4:47915200-47917600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:47915400-47916200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr4:47915400-47916800	Active TSS	HSMM	muscle
33	chr4:47915400-47917000	Active TSS	Hela-S3	cervix
34	chr4:47915400-47917200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:47915400-47917200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:47915400-47917200	Active TSS	Colonic Mucosa	Colon
37	chr4:47915400-47917200	Active TSS	Fetal Kidney	kidney
38	chr4:47915400-47917200	Active TSS	Gastric	stomach
39	chr4:47915400-47917400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr4:47915400-47917400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:47915400-47917600	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr4:47915600-47916200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:47915600-47916400	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr4:47915600-47916800	Active TSS	Osteobl	bone
45	chr4:47915600-47917000	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr4:47915600-47917000	Active TSS	Colon Smooth Muscle	Colon
47	chr4:47915600-47917000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr4:47915600-47917000	Bivalent/Poised TSS	HepG2	liver
49	chr4:47915600-47917000	Active TSS	K562	blood
50	chr4:47915600-47917200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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