Variant report

Variant	rs553353170
Chromosome Location	chr3:42543943-42543944
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	chr3:42543633-42544897	MCF-7	breast:	n/a	n/a
2	SP1	chr3:42543714-42544217	A549	lung:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
3	ELF1	chr3:42543872-42544311	K562	blood:	n/a	n/a
4	PBX3	chr3:42543871-42544308	A549	lung:	n/a	chr3:42544042-42544062
5	POLR2A	chr3:42543814-42544341	HCT-116	colon:	n/a	n/a
6	CTCF	chr3:42543886-42543967	Spleen_OC	spleen:	n/a	n/a
7	SP1	chr3:42543704-42544159	H1-hESC	embryonic stem cell:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
8	JUND	chr3:42543689-42543955	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:42543764-42543977	K562	blood:	n/a	n/a
10	NFYB	chr3:42543735-42544274	GM12878	blood:	n/a	n/a
11	SP2	chr3:42543888-42544322	K562	blood:	n/a	chr3:42544041-42544064 chr3:42543997-42544012 chr3:42544021-42544036
12	HMGN3	chr3:42543813-42544638	K562	blood:	n/a	n/a
13	CREB1	chr3:42543637-42544293	HepG2	liver:	n/a	n/a
14	CCNT2	chr3:42543936-42544338	K562	blood:	n/a	chr3:42544085-42544094 chr3:42543993-42544002
15	TCF7L2	chr3:42543321-42544249	HCT-116	colon:	n/a	n/a
16	SP1	chr3:42543797-42544154	GM12878	blood:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
17	SP1	chr3:42543630-42544284	H1-hESC	embryonic stem cell:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
18	BACH1	chr3:42543207-42544084	H1-hESC	embryonic stem cell:	n/a	n/a
19	SP4	chr3:42543662-42544200	H1-hESC	embryonic stem cell:	n/a	chr3:42543995-42544011 chr3:42544077-42544093
20	CHD2	chr3:42543845-42544207	H1-hESC	embryonic stem cell:	n/a	n/a
21	ATF2	chr3:42543670-42544060	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:42543907-42543945	HUVEC	blood vessel:	n/a	n/a
23	GABPA	chr3:42543828-42544232	MCF-7	breast:	n/a	chr3:42544170-42544179 chr3:42544120-42544134
24	POLR2A	chr3:42543859-42544108	MCF10A-Er-Src	breast:	n/a	n/a
25	PBX3	chr3:42543737-42544351	SK-N-SH	brain:	n/a	chr3:42544042-42544062
26	SP1	chr3:42543728-42544325	K562	blood:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
27	MAX	chr3:42543553-42544349	A549	lung:	n/a	n/a
28	PBX3	chr3:42543941-42544212	GM12878	blood:	n/a	chr3:42544042-42544062
29	TEAD4	chr3:42543730-42544115	H1-hESC	embryonic stem cell:	n/a	chr3:42543860-42543869
30	SP2	chr3:42543807-42544113	HepG2	liver:	n/a	chr3:42544041-42544064 chr3:42543997-42544012 chr3:42544021-42544036
31	SP2	chr3:42543804-42544213	H1-hESC	embryonic stem cell:	n/a	chr3:42544041-42544064 chr3:42543997-42544012 chr3:42544021-42544036
32	ZBTB7A	chr3:42543848-42544222	K562	blood:	n/a	n/a
33	MAX	chr3:42543583-42543954	H1-hESC	embryonic stem cell:	n/a	n/a
34	ZNF143	chr3:42543221-42544185	H1-hESC	embryonic stem cell:	n/a	n/a
35	HA-E2F1	chr3:42543731-42544342	MCF-7	breast:	n/a	chr3:42544079-42544088 chr3:42544023-42544032
36	FOS	chr3:42543864-42544193	K562	blood:	n/a	chr3:42544171-42544180
37	RAD21	chr3:42543902-42544329	H1-hESC	embryonic stem cell:	n/a	chr3:42544081-42544091
38	PBX3	chr3:42543877-42544217	GM12878	blood:	n/a	chr3:42544042-42544062
39	SP1	chr3:42543709-42544311	A549	lung:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
40	CHD2	chr3:42543870-42544191	K562	blood:	n/a	n/a
41	E2F6	chr3:42542766-42544628	H1-hESC	embryonic stem cell:	n/a	chr3:42543156-42543166 chr3:42544079-42544088 chr3:42542968-42542978 chr3:42544023-42544032
42	POLR2A	chr3:42543799-42544454	H1-hESC	embryonic stem cell:	n/a	n/a
43	NFYB	chr3:42543624-42544253	K562	blood:	n/a	n/a
44	MAX	chr3:42543544-42544394	ECC-1	luminal epithelium:	n/a	chr3:42544354-42544364
45	SP4	chr3:42543743-42544238	H1-hESC	embryonic stem cell:	n/a	chr3:42543995-42544011 chr3:42544077-42544093
46	POLR2A	chr3:42543663-42544360	HCT-116	colon:	n/a	n/a
47	POLR2A	chr3:42543596-42544346	H1-neurons	neurons:	n/a	n/a
48	E2F4	chr3:42543843-42544158	MCF10A-Er-Src	breast:	n/a	chr3:42544079-42544088 chr3:42544023-42544032
49	TAF1	chr3:42543741-42544294	H1-hESC	embryonic stem cell:	n/a	n/a
50	GABPA	chr3:42543453-42544340	K562	blood:	n/a	chr3:42544170-42544179 chr3:42544120-42544134

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:42543933-42543983	HepG2	liver:	n/a
2	chr3:42543933-42543983	HAEpiC	amniotic membrane:	n/a
3	chr3:42543933-42543983	AG10803	skin:	n/a
4	chr3:42543933-42543983	GM12891	blood:	n/a
5	chr3:42543933-42543983	GM12892	blood:	n/a
6	chr3:42543933-42543983	HUVEC	blood vessel:	n/a
7	chr3:42543933-42543983	SKMC	muscle:	n/a
8	chr3:42543933-42543983	NHBE	bronchial:	n/a
9	chr3:42543933-42543983	U87	brain:	n/a
10	chr3:42543933-42543983	HEK293	kidney:	embryo
11	chr3:42543933-42543983	AoSMC	blood vessel:	n/a
12	chr3:42543933-42543983	HL-60	blood:	n/a
13	chr3:42543933-42543983	HIPEpiC	eye:	n/a
14	chr3:42543933-42543983	RPTEC	kidney:	n/a
15	chr3:42543933-42543983	HCT-116	colon:	n/a
16	chr3:42543933-42543983	PFSK-1	brain:	n/a
17	chr3:42543933-42543983	HCM	heart:	n/a
18	chr3:42543933-42543983	Hepatocyte	liver:	n/a
19	chr3:42543933-42543983	GM06990	blood:	n/a
20	chr3:42543933-42543983	ProgFib	skin:	n/a
21	chr3:42543933-42543983	NHDF-neo	bronchial:	n/a
22	chr3:42543933-42543983	AG04450	lung:	fetal
23	chr3:42543933-42543983	HEEpiC	esophagus:	n/a
24	chr3:42543933-42543983	SK-N-SH_RA	brain:	n/a
25	chr3:42543933-42543983	NB4	blood:	n/a
26	chr3:42543933-42543983	IMR90	lung:	fetal
27	chr3:42543933-42543983	MCF10A-Er-Src	breast:	n/a
28	chr3:42543933-42543983	HMEC	breast:	n/a
29	chr3:42543933-42543983	PrEC	prostate:	n/a
30	chr3:42543933-42543983	PANC-1	pancreas:	n/a
31	chr3:42543933-42543983	HCPEpiC	choroid plexus:	n/a
32	chr3:42543933-42543983	H1-hESC	embryonic stem cell:	embryo
33	chr3:42543933-42543983	GM19239	blood:	n/a
34	chr3:42543933-42543983	CMK	blood:	n/a
35	chr3:42543933-42543983	HRPEpiC	eye:	n/a
36	chr3:42543933-42543983	K562	blood:	n/a
37	chr3:42543933-42543983	T-47D	breast:	n/a
38	chr3:42543933-42543983	BE2_C	brain:	n/a
39	chr3:42543933-42543983	HRCEpiC	kidney:	n/a
40	chr3:42543933-42543983	NT2-D1	testis:	n/a
41	chr3:42543933-42543983	AG09319	gingival:	n/a
42	chr3:42543933-42543983	AG04449	skin:	fetal
43	chr3:42543933-42543983	GM12878	blood:	n/a
44	chr3:42543933-42543983	HPAEpiC	pulmonary alveolar:	n/a
45	chr3:42543933-42543983	Caco-2	colon:	n/a
46	chr3:42543933-42543983	SK-N-SH	brain:	n/a
47	chr3:42543933-42543983	Jurkat	blood:	n/a
48	chr3:42543933-42543983	A549	lung:	n/a
49	chr3:42543933-42543983	SAEC	small airway:	n/a
50	chr3:42543933-42543983	HNPCEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42529189..42533440-chr3:42542111..42547805,7	MCF-7	breast:
2	chr3:42542597..42545270-chr3:42568668..42571142,2	K562	blood:
3	chr3:42543941..42547920-chr3:42554474..42558044,4	K562	blood:

Variant related genes	Relation type
VIPR1	TF binding region
VIPR1	CpG island
ENSG00000114812	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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3435194	chr3:42543398-42545496	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42542000-42544800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:42542200-42545200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr3:42542400-42544600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:42542600-42544000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
6	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
7	chr3:42542600-42544400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:42542600-42544800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr3:42542600-42545000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr3:42542600-42545200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:42542600-42545200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:42542800-42544000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
14	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
15	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
16	chr3:42542800-42544200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
17	chr3:42542800-42544200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
18	chr3:42542800-42544600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr3:42542800-42544800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
21	chr3:42543000-42544000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
22	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:42543000-42544000	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
26	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
27	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
30	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Thymus	Thymus
31	chr3:42543000-42544200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
32	chr3:42543000-42544200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:42543000-42544400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:42543000-42544400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:42543000-42544400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:42543000-42544600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:42543000-42544600	Active TSS	Aorta	Aorta
38	chr3:42543000-42544800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:42543000-42544800	Active TSS	Left Ventricle	heart
40	chr3:42543000-42545000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:42543200-42544000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:42543200-42544000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr3:42543200-42544000	Flanking Active TSS	Pancreas	Pancrea
44	chr3:42543200-42544000	Flanking Active TSS	Spleen	Spleen
45	chr3:42543200-42544000	Flanking Active TSS	HMEC	breast
46	chr3:42543200-42544000	Flanking Active TSS	NHEK	skin
47	chr3:42543200-42544400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:42543200-42544400	Active TSS	Esophagus	oesophagus
49	chr3:42543200-42544600	Active TSS	Gastric	stomach
50	chr3:42543200-42545200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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