Variant report

Variant	rs77518238
Chromosome Location	chr4:47916233-47916234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:229)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:229 , 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	CTCF	chr4:47916140-47916290	GM12867	blood:	n/a	n/a
2	POLR2A	chr4:47916213-47916377	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:47915779-47917050	H1-hESC	embryonic stem cell:	n/a	n/a
4	PML	chr4:47916137-47916839	K562	blood:	n/a	n/a
5	E2F6	chr4:47916091-47917115	K562	blood:	n/a	chr4:47916758-47916767
6	POLR2A	chr4:47915786-47917044	GM18526	blood:	n/a	n/a
7	RELA	chr4:47915447-47917043	GM15510	blood:	n/a	n/a
8	POLR2A	chr4:47915664-47917000	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr4:47915741-47917060	Hela-S3	cervix:	n/a	n/a
10	SIN3AK20	chr4:47915690-47917128	MCF-7	breast:	n/a	n/a
11	HEY1	chr4:47916205-47916695	K562	blood:	n/a	n/a
12	ZEB1	chr4:47915710-47917010	GM12878	blood:	n/a	chr4:47915954-47915961 chr4:47916921-47916933 chr4:47916923-47916930
13	POLR2A	chr4:47915723-47916962	MCF-7	breast:	n/a	n/a
14	POLR2A	chr4:47915516-47917078	NB4	blood:	n/a	n/a
15	POLR2A	chr4:47915898-47916966	Gliobla	brain:	n/a	n/a
16	ETS1	chr4:47915867-47917087	GM12878	blood:	n/a	chr4:47916789-47916802 chr4:47916793-47916800 chr4:47916788-47916801
17	POLR2A	chr4:47915958-47916747	HepG2	liver:	n/a	n/a
18	ZBTB7A	chr4:47915823-47917124	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr4:47915807-47916761	IMR90	lung:	n/a	n/a
20	POLR2A	chr4:47915717-47916948	MCF-7	breast:	n/a	n/a
21	MAX	chr4:47915367-47917156	Hela-S3	cervix:	n/a	n/a
22	ELF1	chr4:47915759-47916931	GM12878	blood:	n/a	chr4:47915913-47915922
23	POLR2A	chr4:47915370-47917105	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:47916122-47917168	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr4:47916078-47917004	PFSK-1	brain:	n/a	n/a
26	YY1	chr4:47915766-47916251	SK-N-SH_RA	brain:	n/a	chr4:47915913-47915922 chr4:47916135-47916152
27	TCF12	chr4:47916159-47917226	ECC-1	luminal epithelium:	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	CTCF	chr4:47916120-47916270	AG09319	gingival:	n/a	n/a
31	POLR2A	chr4:47915315-47917247	GM12891	blood:	n/a	n/a
32	POLR2A	chr4:47916222-47916761	Hela-S3	cervix:	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	POLR2A	chr4:47916211-47917142	PFSK-1	brain:	n/a	n/a
37	MAX	chr4:47915655-47917169	HCT-116	colon:	n/a	n/a
38	CTCF	chr4:47916148-47916958	GM12878	blood:	n/a	n/a
39	YY1	chr4:47915772-47917056	ECC-1	luminal epithelium:	n/a	chr4:47915913-47915922 chr4:47916966-47916985 chr4:47916135-47916152 chr4:47916971-47916979
40	YY1	chr4:47915887-47916977	SK-N-SH_RA	brain:	n/a	chr4:47915913-47915922 chr4:47916135-47916152
41	TAF1	chr4:47915742-47916776	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:47915794-47917007	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr4:47915842-47916709	A549	lung:	n/a	n/a
44	CTCF	chr4:47916180-47916330	SK-N-SH_RA	brain:	n/a	n/a
45	MXI1	chr4:47915903-47917016	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr4:47915777-47917124	GM12878	blood:	n/a	n/a
47	MAX	chr4:47915718-47917144	A549	lung:	n/a	n/a
48	ZKSCAN1	chr4:47916223-47916967	Hela-S3	cervix:	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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:47916193-47916243	HEK293	kidney:	embryo
2	chr4:47916193-47916243	AG09309	skin:	n/a
3	chr4:47916193-47916243	T-47D	breast:	n/a
4	chr4:47916193-47916243	HL-60	blood:	n/a
5	chr4:47916193-47916243	NH-A	brain:	n/a
6	chr4:47916193-47916243	BJ	skin:	n/a
7	chr4:47916193-47916243	AG10803	skin:	n/a
8	chr4:47916193-47916243	NHDF-neo	bronchial:	n/a
9	chr4:47916193-47916243	Jurkat	blood:	n/a
10	chr4:47916193-47916243	LNCaP	prostate:	n/a
11	chr4:47916193-47916243	ECC-1	luminal epithelium:	n/a
12	chr4:47916193-47916243	HRE	kidney:	n/a
13	chr4:47916193-47916243	AG04450	lung:	fetal
14	chr4:47916193-47916243	ovcar-3	ovarian:	n/a
15	chr4:47916193-47916243	ProgFib	skin:	n/a
16	chr4:47916193-47916243	HAEpiC	amniotic membrane:	n/a
17	chr4:47916193-47916243	HCT-116	colon:	n/a
18	chr4:47916193-47916243	PFSK-1	brain:	n/a
19	chr4:47916193-47916243	BE2_C	brain:	n/a
20	chr4:47916193-47916243	SK-N-SH	brain:	n/a
21	chr4:47916193-47916243	NB4	blood:	n/a
22	chr4:47916193-47916243	SKMC	muscle:	n/a
23	chr4:47916193-47916243	SK-N-SH_RA	brain:	n/a
24	chr4:47916193-47916243	GM12892	blood:	n/a
25	chr4:47916193-47916243	Caco-2	colon:	n/a
26	chr4:47916193-47916243	SAEC	small airway:	n/a
27	chr4:47916193-47916243	HCF	heart:	n/a
28	chr4:47916193-47916243	AG09319	gingival:	n/a
29	chr4:47916193-47916243	Hepatocyte	liver:	n/a
30	chr4:47916193-47916243	HMEC	breast:	n/a
31	chr4:47916193-47916243	SK-N-MC	brain:	n/a
32	chr4:47916193-47916243	HCM	heart:	n/a
33	chr4:47916193-47916243	RPTEC	kidney:	n/a
34	chr4:47916193-47916243	U87	brain:	n/a
35	chr4:47916193-47916243	NT2-D1	testis:	n/a
36	chr4:47916193-47916243	A549	lung:	n/a
37	chr4:47916193-47916243	AG04449	skin:	fetal
38	chr4:47916193-47916243	MCF10A-Er-Src	breast:	n/a
39	chr4:47916193-47916243	GM12878	blood:	n/a
40	chr4:47916193-47916243	K562	blood:	n/a
41	chr4:47916193-47916243	HRPEpiC	eye:	n/a
42	chr4:47916193-47916243	PrEC	prostate:	n/a
43	chr4:47916193-47916243	HPAEpiC	pulmonary alveolar:	n/a
44	chr4:47916193-47916243	NHBE	bronchial:	n/a
45	chr4:47916193-47916243	IMR90	lung:	fetal
46	chr4:47916193-47916243	MCF-7	breast:	n/a
47	chr4:47916193-47916243	HRCEpiC	kidney:	n/a
48	chr4:47916193-47916243	H1-hESC	embryonic stem cell:	embryo
49	chr4:47916193-47916243	HepG2	liver:	n/a
50	chr4:47916193-47916243	AoSMC	blood vessel:	n/a

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

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

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NIPAL1-1	chr4:47916159-47916721	NONHSAT096273
2	lnc-NIPAL1-1	chr4:47915823-47916721	NONHSAT096272

No data

Variant related genes	Relation type
NIPAL1	TF binding region
NIPAL1	CpG island
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	chr4:47915200-47916400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr4:47915200-47916400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:47915200-47917200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:47915200-47917200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:47915200-47917200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:47915200-47917200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:47915200-47917200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:47915200-47917200	Active TSS	Aorta	Aorta
21	chr4:47915200-47917200	Active TSS	Pancreas	Pancrea
22	chr4:47915200-47917200	Active TSS	Psoas Muscle	Psoas
23	chr4:47915200-47917400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:47915200-47917400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:47915200-47917400	Active TSS	Brain Germinal Matrix	brain
26	chr4:47915200-47917600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:47915400-47916800	Active TSS	HSMM	muscle
28	chr4:47915400-47917000	Active TSS	Hela-S3	cervix
29	chr4:47915400-47917200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:47915400-47917200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:47915400-47917200	Active TSS	Colonic Mucosa	Colon
32	chr4:47915400-47917200	Active TSS	Fetal Kidney	kidney
33	chr4:47915400-47917200	Active TSS	Gastric	stomach
34	chr4:47915400-47917400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr4:47915400-47917400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:47915400-47917600	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr4:47915600-47916400	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr4:47915600-47916800	Active TSS	Osteobl	bone
39	chr4:47915600-47917000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr4:47915600-47917000	Active TSS	Colon Smooth Muscle	Colon
41	chr4:47915600-47917000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr4:47915600-47917000	Bivalent/Poised TSS	HepG2	liver
43	chr4:47915600-47917000	Active TSS	K562	blood
44	chr4:47915600-47917200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:47915600-47917200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:47915600-47917200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:47915600-47917200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:47915600-47917200	Active TSS	Placenta	Placenta
49	chr4:47915600-47917200	Active TSS	Left Ventricle	heart
50	chr4:47915600-47917200	Active TSS	Ovary	ovary

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