Variant report

Variant	rs549524712
Chromosome Location	chr3:135684511-135684512
allele	-/GAGGAGGAGGAG
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	chr3:135684190-135685235	HEK293	kidney:	n/a	n/a
2	ELF1	chr3:135684258-135684602	K562	blood:	n/a	chr3:135684573-135684585
3	POLR2A	chr3:135684498-135684786	A549	lung:	n/a	n/a
4	POLR2A	chr3:135684466-135684760	U87	brain:	n/a	n/a
5	HCFC1	chr3:135684264-135684557	K562	blood:	n/a	n/a
6	TEAD4	chr3:135684474-135685167	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:135684270-135685538	H1-neurons	neurons:	n/a	n/a
8	EGR1	chr3:135684303-135684650	K562	blood:	n/a	n/a
9	POLR2A	chr3:135684172-135685552	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:135684160-135685338	MCF10A-Er-Src	breast:	n/a	n/a
11	MAX	chr3:135684191-135685234	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr3:135684172-135685287	IMR90	lung:	n/a	n/a
13	POLR2A	chr3:135684044-135685250	SK-N-MC	brain:	n/a	n/a
14	MAX	chr3:135684150-135685093	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr3:135684473-135684817	H1-neurons	neurons:	n/a	n/a
16	MYC	chr3:135684367-135684701	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr3:135684290-135685323	U87	brain:	n/a	n/a
18	SP1	chr3:135683988-135684635	A549	lung:	n/a	n/a
19	POLR2A	chr3:135684242-135685245	HUVEC	blood vessel:	n/a	n/a
20	NFIC	chr3:135684172-135684881	ECC-1	luminal epithelium:	n/a	n/a
21	SIN3AK20	chr3:135684486-135684908	PANC-1	pancreas:	n/a	n/a
22	HA-E2F1	chr3:135683924-135685494	MCF-7	breast:	n/a	chr3:135685348-135685358 chr3:135684990-135685000 chr3:135685345-135685355 chr3:135685327-135685339 chr3:135685325-135685340 chr3:135685152-135685161 chr3:135685149-135685161
23	SIN3A	chr3:135684082-135685864	H1-hESC	embryonic stem cell:	n/a	n/a
24	MXI1	chr3:135683801-135686083	SK-N-SH	brain:	n/a	n/a
25	HMGN3	chr3:135684186-135685432	K562	blood:	n/a	n/a
26	SIN3AK20	chr3:135684024-135685525	MCF-7	breast:	n/a	n/a
27	POLR2A	chr3:135684450-135684766	A549	lung:	n/a	n/a
28	EGR1	chr3:135684063-135685430	HCT-116	colon:	n/a	chr3:135685153-135685166 chr3:135684987-135685000 chr3:135684987-135685000 chr3:135684990-135685000 chr3:135684983-135685005 chr3:135685270-135685280 chr3:135684987-135685000 chr3:135684988-135684999 chr3:135684990-135684999 chr3:135684987-135685000
29	POLR2A	chr3:135684103-135685314	MCF-7	breast:	n/a	n/a
30	POLR2A	chr3:135684474-135685156	A549	lung:	n/a	n/a
31	MAX	chr3:135684318-135685250	SK-N-SH	brain:	n/a	n/a
32	SP4	chr3:135684069-135684797	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr3:135684012-135685177	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr3:135684474-135684766	SK-N-SH	brain:	n/a	n/a
35	CHD2	chr3:135684198-135684785	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:135684106-135685323	MCF-7	breast:	n/a	n/a
37	EGR1	chr3:135684028-135685374	HCT-116	colon:	n/a	chr3:135685153-135685166 chr3:135684987-135685000 chr3:135684987-135685000 chr3:135684990-135685000 chr3:135684983-135685005 chr3:135685270-135685280 chr3:135684987-135685000 chr3:135684988-135684999 chr3:135684990-135684999 chr3:135684987-135685000
38	TCF12	chr3:135684047-135685266	ECC-1	luminal epithelium:	n/a	n/a
39	ZBTB7A	chr3:135684254-135684618	K562	blood:	n/a	chr3:135684304-135684315
40	TAF1	chr3:135684460-135685568	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr3:135684488-135684761	K562	blood:	n/a	n/a
42	POLR2A	chr3:135684477-135684710	K562	blood:	n/a	n/a
43	POLR2A	chr3:135684041-135685231	HCT-116	colon:	n/a	n/a
44	POLR2A	chr3:135684197-135685296	MCF-7	breast:	n/a	n/a
45	ZNF263	chr3:135684127-135686042	HEK293-T-REx	kidney:	n/a	n/a
46	POLR2A	chr3:135684465-135685030	H1-hESC	embryonic stem cell:	n/a	n/a
47	REST	chr3:135684212-135686249	H1-neurons	neurons:	n/a	chr3:135685282-135685296
48	MYC	chr3:135684324-135685061	MCF-7	breast:	n/a	n/a
49	MAZ	chr3:135684344-135684720	GM12878	blood:	n/a	n/a
50	SIN3AK20	chr3:135684057-135684676	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:135684468-135684518	HRPEpiC	eye:	n/a
2	chr3:135684466-135684516	HPAEpiC	pulmonary alveolar:	n/a
3	chr3:135684466-135684516	A549	lung:	n/a
4	chr3:135684468-135684518	SK-N-SH_RA	brain:	n/a
5	chr3:135684468-135684518	AG04449	skin:	fetal
6	chr3:135684468-135684518	AG10803	skin:	n/a
7	chr3:135684466-135684516	AG10803	skin:	n/a
8	chr3:135684468-135684518	HRCEpiC	kidney:	n/a
9	chr3:135684468-135684518	HIPEpiC	eye:	n/a
10	chr3:135684468-135684518	GM06990	blood:	n/a
11	chr3:135684466-135684516	Jurkat	blood:	n/a
12	chr3:135684466-135684516	BJ	skin:	n/a
13	chr3:135684466-135684516	HIPEpiC	eye:	n/a
14	chr3:135684468-135684518	HCF	heart:	n/a
15	chr3:135684468-135684518	SK-N-SH	brain:	n/a
16	chr3:135684466-135684516	AG04449	skin:	fetal
17	chr3:135684466-135684516	BE2_C	brain:	n/a
18	chr3:135684466-135684516	HRCEpiC	kidney:	n/a
19	chr3:135684468-135684518	AG09309	skin:	n/a
20	chr3:135684468-135684518	U87	brain:	n/a
21	chr3:135684466-135684516	HCPEpiC	choroid plexus:	n/a
22	chr3:135684468-135684518	SK-N-MC	brain:	n/a
23	chr3:135684468-135684518	LNCaP	prostate:	n/a
24	chr3:135684466-135684516	MCF-7	breast:	n/a
25	chr3:135684466-135684516	GM19239	blood:	n/a
26	chr3:135684466-135684516	HepG2	liver:	n/a
27	chr3:135684468-135684518	Hepatocyte	liver:	n/a
28	chr3:135684466-135684516	HEK293	kidney:	embryo
29	chr3:135684468-135684518	HCPEpiC	choroid plexus:	n/a
30	chr3:135684468-135684518	HepG2	liver:	n/a
31	chr3:135684466-135684516	Caco-2	colon:	n/a
32	chr3:135684466-135684516	PFSK-1	brain:	n/a
33	chr3:135684466-135684516	SKMC	muscle:	n/a
34	chr3:135684468-135684518	HRE	kidney:	n/a
35	chr3:135684468-135684518	NB4	blood:	n/a
36	chr3:135684468-135684518	GM12892	blood:	n/a
37	chr3:135684468-135684518	HUVEC	blood vessel:	n/a
38	chr3:135684468-135684518	K562	blood:	n/a
39	chr3:135684466-135684516	HMEC	breast:	n/a
40	chr3:135684468-135684518	PANC-1	pancreas:	n/a
41	chr3:135684468-135684518	HL-60	blood:	n/a
42	chr3:135684468-135684518	NT2-D1	testis:	n/a
43	chr3:135684466-135684516	SK-N-SH	brain:	n/a
44	chr3:135684468-135684518	NHDF-neo	bronchial:	n/a
45	chr3:135684468-135684518	IMR90	lung:	fetal
46	chr3:135684468-135684518	NH-A	brain:	n/a
47	chr3:135684466-135684516	HCF	heart:	n/a
48	chr3:135684466-135684516	HRE	kidney:	n/a
49	chr3:135684468-135684518	BE2_C	brain:	n/a
50	chr3:135684468-135684518	H1-hESC	embryonic stem cell:	embryo

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135683335..135686243-chr3:135740274..135744209,4	MCF-7	breast:
2	chr3:135678002..135681918-chr3:135682555..135686339,5	MCF-7	breast:

Variant related genes	Relation type
PPP2R3A	TF binding region
PPP2R3A	CpG island
ENSG00000241905	Chromatin interaction
ENSG00000073711	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	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv3374702	chr3:135649303-135686527	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3393718	chr3:135683487-135686235	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135682800-135684600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:135683000-135685800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:135683800-135685000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
4	chr3:135683800-135685000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
5	chr3:135683800-135685800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:135683800-135686200	Active TSS	HSMMtube	muscle
7	chr3:135683800-135687200	Active TSS	Stomach Smooth Muscle	stomach
8	chr3:135684000-135684800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:135684000-135684800	Active TSS	Brain Germinal Matrix	brain
10	chr3:135684000-135685000	Active TSS	Primary hematopoietic stem cells	blood
11	chr3:135684000-135685000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:135684000-135685000	Bivalent/Poised TSS	Thymus	Thymus
13	chr3:135684000-135685200	Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr3:135684000-135685200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:135684000-135685200	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr3:135684000-135685400	Active TSS	Primary T cells from cord blood	blood
17	chr3:135684000-135685400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:135684000-135685400	Active TSS	Fetal Lung	lung
19	chr3:135684000-135685600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:135684000-135685600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:135684000-135685600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:135684000-135685600	Active TSS	Brain Angular Gyrus	brain
23	chr3:135684000-135685600	Active TSS	Brain Anterior Caudate	brain
24	chr3:135684000-135685600	Active TSS	Brain Cingulate Gyrus	brain
25	chr3:135684000-135685600	Active TSS	Brain Hippocampus Middle	brain
26	chr3:135684000-135685600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr3:135684000-135685600	Active TSS	Fetal Stomach	stomach
28	chr3:135684000-135685600	Active TSS	Left Ventricle	heart
29	chr3:135684000-135685600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr3:135684000-135685600	Active TSS	HMEC	breast
31	chr3:135684000-135685600	Active TSS	K562	blood
32	chr3:135684000-135685600	Active TSS	NH-A	brain
33	chr3:135684000-135685600	Active TSS	Osteobl	bone
34	chr3:135684000-135685800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:135684000-135685800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr3:135684000-135685800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:135684000-135685800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:135684000-135685800	Active TSS	Muscle Satellite Cultured Cells	--
39	chr3:135684000-135685800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:135684000-135685800	Active TSS	Brain Substantia Nigra	brain
41	chr3:135684000-135685800	Active TSS	Esophagus	oesophagus
42	chr3:135684000-135685800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr3:135684000-135685800	Active TSS	Psoas Muscle	Psoas
44	chr3:135684000-135686000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:135684000-135686000	Active TSS	Colonic Mucosa	Colon
46	chr3:135684000-135686000	Active TSS	Ovary	ovary
47	chr3:135684000-135686000	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:135684000-135686000	Active TSS	A549	lung
49	chr3:135684000-135686000	Active TSS	NHDF-Ad	bronchial
50	chr3:135684000-135686200	Active TSS	iPS-15b Cell Line	embryonic stem cell

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