Variant report

Variant	rs561743547
Chromosome Location	chr5:37840109-37840110
allele	A/C
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	chr5:37839792-37840931	IMR90	lung:	n/a	n/a
2	CTBP2	chr5:37839040-37840731	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr5:37839598-37840171	H1-hESC	embryonic stem cell:	n/a	chr5:37839794-37839804 chr5:37839800-37839810 chr5:37839797-37839807 chr5:37839877-37839887
4	RAD21	chr5:37839833-37841082	IMR90	lung:	n/a	chr5:37840712-37840722 chr5:37840433-37840446
5	HDAC2	chr5:37839830-37840138	HepG2	liver:	n/a	n/a
6	CTCF	chr5:37839925-37840128	MCF-7	breast:	n/a	n/a
7	POLR2A	chr5:37839902-37840121	SK-N-SH	brain:	n/a	n/a
8	MAX	chr5:37839899-37840151	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr5:37839743-37840858	A549	lung:	n/a	chr5:37840289-37840299
10	CTCF	chr5:37840000-37840290	NHDF-neo	bronchial:	n/a	n/a
11	CTCF	chr5:37839980-37840130	BJ	skin:	n/a	n/a
12	MAX	chr5:37839803-37840190	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr5:37839960-37840110	SAEC	small airway:	n/a	n/a
14	ZNF263	chr5:37839746-37841001	HEK293-T-REx	kidney:	n/a	chr5:37840249-37840258
15	BHLHE40	chr5:37839864-37840661	HepG2	liver:	n/a	chr5:37839968-37839984 chr5:37839973-37839989 chr5:37839947-37839963
16	MAX	chr5:37839808-37840269	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr5:37839740-37840787	HepG2	liver:	n/a	chr5:37840289-37840299
18	MXI1	chr5:37839252-37840328	IMR90	lung:	n/a	chr5:37839378-37839387
19	SIN3AK20	chr5:37839881-37840161	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr5:37839960-37840110	HEEpiC	esophagus:	n/a	n/a
21	MAX	chr5:37839785-37840217	MCF-7	breast:	n/a	n/a
22	MAZ	chr5:37838894-37841199	IMR90	lung:	n/a	chr5:37839592-37839602 chr5:37840289-37840299 chr5:37839378-37839388 chr5:37839135-37839145
23	HA-E2F1	chr5:37839600-37840974	MCF-7	breast:	n/a	chr5:37839794-37839804 chr5:37840192-37840201 chr5:37839800-37839810 chr5:37839797-37839807 chr5:37839877-37839887 chr5:37840472-37840482
24	CTCF	chr5:37839870-37840127	IMR90	lung:	n/a	n/a
25	POLR2A	chr5:37839876-37841002	ProgFib	skin:	n/a	n/a
26	MAX	chr5:37839552-37840816	H1-hESC	embryonic stem cell:	n/a	chr5:37839592-37839602 chr5:37840289-37840299
27	MAX	chr5:37839844-37840314	SK-N-SH	brain:	n/a	chr5:37840289-37840299
28	CTCF	chr5:37839960-37840110	HCFaa	heart:	n/a	n/a
29	POLR2A	chr5:37839943-37841081	U87	brain:	n/a	n/a
30	CTCF	chr5:37839960-37840110	HMEC	breast:	n/a	n/a
31	CTCF	chr5:37839980-37840130	HEK293	kidney:	n/a	n/a
32	CTCF	chr5:37839960-37840110	HEK293	kidney:	n/a	n/a
33	CTCF	chr5:37840040-37840190	HRE	kidney:	n/a	n/a
34	CTCF	chr5:37840000-37840150	HRE	kidney:	n/a	n/a
35	MAX	chr5:37839843-37840165	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr5:37839840-37840196	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr5:37839787-37840262	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr5:37839866-37840118	U87	brain:	n/a	n/a
39	E2F6	chr5:37836391-37840195	H1-hESC	embryonic stem cell:	n/a	chr5:37838340-37838347 chr5:37838955-37838964 chr5:37838113-37838121 chr5:37838400-37838407 chr5:37839794-37839804 chr5:37838739-37838747 chr5:37836831-37836840 chr5:37839800-37839810 chr5:37839797-37839807 chr5:37839877-37839887 chr5:37837060-37837072 chr5:37838340-37838347 chr5:37838739-37838747 chr5:37838112-37838122 chr5:37838663-37838672 chr5:37838113-37838120 chr5:37838340-37838347 chr5:37838113-37838121 chr5:37838112-37838123
40	CTCF	chr5:37839960-37840110	HMF	breast:	n/a	n/a
41	POLR2A	chr5:37839866-37840171	U87	brain:	n/a	n/a
42	MYC	chr5:37839951-37840114	MCF-7	breast:	n/a	n/a
43	POLR2A	chr5:37839937-37841084	U87	brain:	n/a	n/a
44	MAX	chr5:37839864-37840119	HepG2	liver:	n/a	n/a
45	CTCF	chr5:37839980-37840130	GM12865	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:37840089-37840139	NHBE	bronchial:	n/a
2	chr5:37840075-37840125	PrEC	prostate:	n/a
3	chr5:37840075-37840125	HIPEpiC	eye:	n/a
4	chr5:37840075-37840125	RPTEC	kidney:	n/a
5	chr5:37840089-37840139	NHDF-neo	bronchial:	n/a
6	chr5:37840075-37840125	Caco-2	colon:	n/a
7	chr5:37840075-37840125	NT2-D1	testis:	n/a
8	chr5:37840075-37840125	NHBE	bronchial:	n/a
9	chr5:37840089-37840139	HMEC	breast:	n/a
10	chr5:37840075-37840125	Hela-S3	cervix:	n/a
11	chr5:37840089-37840139	AoSMC	blood vessel:	n/a
12	chr5:37840089-37840139	SK-N-MC	brain:	n/a
13	chr5:37840089-37840139	AG09319	gingival:	n/a
14	chr5:37840075-37840125	A549	lung:	n/a
15	chr5:37840075-37840125	HRCEpiC	kidney:	n/a
16	chr5:37840089-37840139	HL-60	blood:	n/a
17	chr5:37840075-37840125	BE2_C	brain:	n/a
18	chr5:37840089-37840139	LNCaP	prostate:	n/a
19	chr5:37840075-37840125	GM12878	blood:	n/a
20	chr5:37840075-37840125	H1-hESC	embryonic stem cell:	embryo
21	chr5:37840075-37840125	HNPCEpiC	eye:	n/a
22	chr5:37840089-37840139	NT2-D1	testis:	n/a
23	chr5:37840075-37840125	HepG2	liver:	n/a
24	chr5:37840075-37840125	ProgFib	skin:	n/a
25	chr5:37840075-37840125	AG10803	skin:	n/a
26	chr5:37840089-37840139	HCF	heart:	n/a
27	chr5:37840075-37840125	BJ	skin:	n/a
28	chr5:37840075-37840125	ECC-1	luminal epithelium:	n/a
29	chr5:37840089-37840139	HCPEpiC	choroid plexus:	n/a
30	chr5:37840075-37840125	ovcar-3	ovarian:	n/a
31	chr5:37840089-37840139	ECC-1	luminal epithelium:	n/a
32	chr5:37840089-37840139	T-47D	breast:	n/a
33	chr5:37840089-37840139	HRCEpiC	kidney:	n/a
34	chr5:37840075-37840125	T-47D	breast:	n/a
35	chr5:37840089-37840139	H1-hESC	embryonic stem cell:	embryo
36	chr5:37840089-37840139	U87	brain:	n/a
37	chr5:37840089-37840139	SKMC	muscle:	n/a
38	chr5:37840089-37840139	HPAEpiC	pulmonary alveolar:	n/a
39	chr5:37840075-37840125	GM06990	blood:	n/a
40	chr5:37840075-37840125	NHDF-neo	bronchial:	n/a
41	chr5:37840075-37840125	AG09309	skin:	n/a
42	chr5:37840089-37840139	SK-N-SH_RA	brain:	n/a
43	chr5:37840089-37840139	Hepatocyte	liver:	n/a
44	chr5:37840075-37840125	U87	brain:	n/a
45	chr5:37840075-37840125	LNCaP	prostate:	n/a
46	chr5:37840089-37840139	HCM	heart:	n/a
47	chr5:37840075-37840125	MCF-7	breast:	n/a
48	chr5:37840089-37840139	HEEpiC	esophagus:	n/a
49	chr5:37840089-37840139	HAEpiC	amniotic membrane:	n/a
50	chr5:37840075-37840125	HRPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37834038..37837439-chr5:37839505..37841588,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR70-1	chr5:37839970-37840675	NONHSAT101070

Variant related genes	Relation type
GDNF-AS1	TF binding region
GDNF	TF binding region
GDNF	CpG island
GDNF-AS1	CpG island
ENSG00000168621	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv1844348	chr5:37835398-37840642	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1851519	chr5:37835398-37840642	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3406944	chr5:37838720-37841568	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1833785	chr5:37839618-37840621	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1838210	chr5:37839618-37840621	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1839230	chr5:37839618-37840621	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1840288	chr5:37839618-37840621	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv597849	chr5:37839618-37840642	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1848849	chr5:37839618-37841045	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1850800	chr5:37839618-37841045	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv13245	chr5:37839636-37840756	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv597850	chr5:37839726-37840243	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv1821997	chr5:37839726-37841045	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv597851	chr5:37839777-37840352	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv597852	chr5:37839885-37840407	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv597853	chr5:37839936-37840509	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv597854	chr5:37840054-37840642	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37834200-37841000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:37834400-37840600	Bivalent Enhancer	Fetal Brain Male	brain
3	chr5:37834400-37841400	Bivalent/Poised TSS	Colonic Mucosa	Colon
4	chr5:37836200-37840200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:37836200-37840600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
6	chr5:37836200-37840800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr5:37836200-37840800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr5:37836200-37840800	Active TSS	NHDF-Ad	bronchial
9	chr5:37836200-37841000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr5:37836200-37841000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:37836400-37840600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:37836400-37840600	Active TSS	HSMM	muscle
13	chr5:37836400-37840800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr5:37836400-37841200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr5:37836400-37841600	Active TSS	HSMMtube	muscle
16	chr5:37836600-37840200	Enhancers	Lung	lung
17	chr5:37836600-37841000	Flanking Active TSS	HMEC	breast
18	chr5:37837000-37840600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr5:37837000-37840800	Active TSS	Osteobl	bone
20	chr5:37838000-37841200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr5:37838200-37841400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
22	chr5:37838400-37840800	Active TSS	Rectal Smooth Muscle	rectum
23	chr5:37838400-37841000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:37838600-37840200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:37838600-37841000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:37838600-37841000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
27	chr5:37839200-37840200	Flanking Bivalent TSS/Enh	Right Ventricle	heart
28	chr5:37839200-37840600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
29	chr5:37839200-37840800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr5:37839200-37840800	Active TSS	Colon Smooth Muscle	Colon
31	chr5:37839200-37841000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:37839400-37840400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr5:37839400-37840400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:37839400-37840600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:37839400-37840600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:37839400-37840600	Active TSS	Fetal Kidney	kidney
37	chr5:37839400-37840800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:37839400-37841000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:37839600-37840200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:37839600-37840200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
41	chr5:37839600-37840400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:37839600-37840400	Bivalent/Poised TSS	Fetal Brain Female	brain
43	chr5:37839600-37840600	Active TSS	Brain Cingulate Gyrus	brain
44	chr5:37839600-37840600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr5:37839600-37840600	Bivalent/Poised TSS	Esophagus	oesophagus
46	chr5:37839600-37840600	Active TSS	NHEK	skin
47	chr5:37839600-37840800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:37839600-37840800	Active TSS	Brain Angular Gyrus	brain
49	chr5:37839600-37840800	Active TSS	Brain Substantia Nigra	brain
50	chr5:37839600-37840800	Bivalent/Poised TSS	Fetal Stomach	stomach

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