Variant report

Variant	rs552921536
Chromosome Location	chr3:142164849-142164850
allele	C/G
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	IRF1	chr3:142164528-142165312	K562	blood:	n/a	chr3:142164956-142164966 chr3:142164989-142165003 chr3:142164956-142164970 chr3:142164962-142164972 chr3:142164955-142164969 chr3:142164954-142164968 chr3:142164950-142164971 chr3:142164952-142164966 chr3:142164985-142164999 chr3:142164987-142165000 chr3:142164986-142165000 chr3:142164954-142164965 chr3:142164955-142164968 chr3:142164955-142164968 chr3:142164989-142165000 chr3:142164958-142164972 chr3:142164954-142164974 chr3:142164989-142164999
2	CREB1	chr3:142164701-142165328	GM12878	blood:	n/a	n/a
3	STAT3	chr3:142164774-142165212	MCF10A-Er-Src	breast:	n/a	chr3:142165028-142165036 chr3:142164955-142164966 chr3:142165022-142165042
4	IRF1	chr3:142164786-142165110	K562	blood:	n/a	chr3:142164956-142164966 chr3:142164989-142165003 chr3:142164956-142164970 chr3:142164962-142164972 chr3:142164955-142164969 chr3:142164954-142164968 chr3:142164950-142164971 chr3:142164952-142164966 chr3:142164985-142164999 chr3:142164987-142165000 chr3:142164986-142165000 chr3:142164954-142164965 chr3:142164955-142164968 chr3:142164955-142164968 chr3:142164989-142165000 chr3:142164958-142164972 chr3:142164954-142164974 chr3:142164989-142164999
5	RUNX3	chr3:142164588-142165210	GM12878	blood:	n/a	n/a
6	CHD1	chr3:142164554-142165575	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:142164605-142167361	GM12891	blood:	n/a	n/a
8	ARID3A	chr3:142164561-142164907	HepG2	liver:	n/a	n/a
9	STAT3	chr3:142164836-142165203	MCF10A-Er-Src	breast:	n/a	chr3:142165028-142165036 chr3:142164955-142164966 chr3:142165022-142165042
10	STAT2	chr3:142164735-142165163	K562	blood:	n/a	chr3:142165028-142165036 chr3:142164955-142164966 chr3:142165022-142165042 chr3:142164952-142164967
11	BATF	chr3:142164703-142164947	GM12878	blood:	n/a	n/a
12	USF1	chr3:142164711-142164989	SK-N-SH_RA	brain:	n/a	n/a
13	STAT3	chr3:142164729-142165182	GM12878	blood:	n/a	chr3:142165028-142165036 chr3:142164955-142164966 chr3:142165022-142165042
14	POLR2A	chr3:142164614-142167252	GM19099	blood:	n/a	n/a
15	IRF1	chr3:142164759-142165640	K562	blood:	n/a	chr3:142164956-142164966 chr3:142164989-142165003 chr3:142164956-142164970 chr3:142164962-142164972 chr3:142164955-142164969 chr3:142164954-142164968 chr3:142164950-142164971 chr3:142164952-142164966 chr3:142164985-142164999 chr3:142164987-142165000 chr3:142165513-142165525 chr3:142165552-142165566 chr3:142164986-142165000 chr3:142164954-142164965 chr3:142164955-142164968 chr3:142164955-142164968 chr3:142164989-142165000 chr3:142164958-142164972 chr3:142164954-142164974 chr3:142165303-142165319 chr3:142164989-142164999 chr3:142165552-142165565
16	IKZF1	chr3:142164721-142165203	GM12878	blood:	n/a	n/a
17	ATF2	chr3:142164617-142165188	GM12878	blood:	n/a	n/a
18	FOS	chr3:142164845-142165116	MCF10A-Er-Src	breast:	n/a	n/a
19	USF2	chr3:142164800-142165008	Hela-S3	cervix:	n/a	n/a
20	MXI1	chr3:142164504-142165213	GM12878	blood:	n/a	n/a
21	STAT3	chr3:142164800-142165198	MCF10A-Er-Src	breast:	n/a	chr3:142165028-142165036 chr3:142164955-142164966 chr3:142165022-142165042
22	RUNX3	chr3:142164757-142165160	GM12878	blood:	n/a	n/a
23	NFIC	chr3:142164614-142165218	GM12878	blood:	n/a	n/a
24	EBF1	chr3:142164768-142165070	GM12878	blood:	n/a	n/a
25	STAT3	chr3:142164829-142165143	Hela-S3	cervix:	n/a	chr3:142165028-142165036 chr3:142164955-142164966 chr3:142165022-142165042
26	TBL1XR1	chr3:142164738-142165095	GM12878	blood:	n/a	n/a
27	SPI1	chr3:142164823-142165215	HL-60	blood:	n/a	n/a
28	SIN3A	chr3:142164751-142165067	GM12878	blood:	n/a	n/a
29	IRF4	chr3:142164603-142165115	GM12878	blood:	n/a	chr3:142164950-142164971
30	STAT1	chr3:142164794-142164897	GM12878	blood:	n/a	n/a
31	STAT3	chr3:142164769-142165084	MCF10A-Er-Src	breast:	n/a	chr3:142165028-142165036 chr3:142164955-142164966 chr3:142165022-142165042
32	TBP	chr3:142164752-142165184	GM12878	blood:	n/a	n/a
33	WRNIP1	chr3:142164477-142164858	GM12878	blood:	n/a	n/a
34	MAX	chr3:142164758-142165039	GM12878	blood:	n/a	n/a
35	USF2	chr3:142164721-142165042	GM12878	blood:	n/a	n/a
36	BATF	chr3:142164672-142165015	GM12878	blood:	n/a	n/a
37	ZNF143	chr3:142164728-142164981	GM12878	blood:	n/a	n/a
38	CUX1	chr3:142164761-142165267	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142164840-142164890	HCF	heart:	n/a
2	chr3:142164840-142164890	NH-A	brain:	n/a
3	chr3:142164840-142164890	AG04450	lung:	fetal
4	chr3:142164840-142164890	HRE	kidney:	n/a
5	chr3:142164840-142164890	ovcar-3	ovarian:	n/a
6	chr3:142164840-142164890	HCPEpiC	choroid plexus:	n/a
7	chr3:142164840-142164890	SKMC	muscle:	n/a
8	chr3:142164840-142164890	HAEpiC	amniotic membrane:	n/a
9	chr3:142164840-142164890	Caco-2	colon:	n/a
10	chr3:142164840-142164890	AG09319	gingival:	n/a
11	chr3:142164840-142164890	SK-N-SH	brain:	n/a
12	chr3:142164840-142164890	HEK293	kidney:	embryo
13	chr3:142164840-142164890	HNPCEpiC	eye:	n/a
14	chr3:142164840-142164890	GM12892	blood:	n/a
15	chr3:142164840-142164890	BE2_C	brain:	n/a
16	chr3:142164840-142164890	HL-60	blood:	n/a
17	chr3:142164840-142164890	K562	blood:	n/a
18	chr3:142164840-142164890	HPAEpiC	pulmonary alveolar:	n/a
19	chr3:142164840-142164890	NHDF-neo	bronchial:	n/a
20	chr3:142164840-142164890	NB4	blood:	n/a
21	chr3:142164840-142164890	ProgFib	skin:	n/a
22	chr3:142164840-142164890	MCF-7	breast:	n/a
23	chr3:142164840-142164890	LNCaP	prostate:	n/a
24	chr3:142164840-142164890	SK-N-MC	brain:	n/a
25	chr3:142164840-142164890	HepG2	liver:	n/a
26	chr3:142164840-142164890	Jurkat	blood:	n/a
27	chr3:142164840-142164890	IMR90	lung:	fetal
28	chr3:142164840-142164890	NHBE	bronchial:	n/a
29	chr3:142164840-142164890	HRCEpiC	kidney:	n/a
30	chr3:142164840-142164890	SAEC	small airway:	n/a
31	chr3:142164840-142164890	AG10803	skin:	n/a
32	chr3:142164840-142164890	MCF10A-Er-Src	breast:	n/a
33	chr3:142164840-142164890	PANC-1	pancreas:	n/a
34	chr3:142164840-142164890	HCT-116	colon:	n/a
35	chr3:142164840-142164890	PrEC	prostate:	n/a
36	chr3:142164840-142164890	T-47D	breast:	n/a
37	chr3:142164840-142164890	GM12878	blood:	n/a
38	chr3:142164840-142164890	PFSK-1	brain:	n/a
39	chr3:142164840-142164890	BJ	skin:	n/a
40	chr3:142164840-142164890	HEEpiC	esophagus:	n/a
41	chr3:142164840-142164890	RPTEC	kidney:	n/a
42	chr3:142164840-142164890	ECC-1	luminal epithelium:	n/a
43	chr3:142164840-142164890	Hepatocyte	liver:	n/a
44	chr3:142164840-142164890	SK-N-SH_RA	brain:	n/a
45	chr3:142164840-142164890	HRPEpiC	eye:	n/a
46	chr3:142164840-142164890	HUVEC	blood vessel:	n/a
47	chr3:142164840-142164890	GM19239	blood:	n/a
48	chr3:142164840-142164890	HCM	heart:	n/a
49	chr3:142164840-142164890	AG04449	skin:	fetal
50	chr3:142164840-142164890	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142164147..142165687-chr3:142176096..142178245,2	K562	blood:
2	chr3:142164765..142166960-chr3:142189962..142191863,2	K562	blood:

Variant related genes	Relation type
ENSG00000242479	TF binding region
ENSG00000242479	CpG island
ENSG00000244327	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142142200-142165400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:142149800-142165000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:142150600-142165400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:142154600-142166000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:142160000-142166000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:142160800-142165400	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:142163000-142165400	Weak transcription	Placenta	Placenta
8	chr3:142163200-142165200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:142163200-142167400	Active TSS	GM12878-XiMat	blood
10	chr3:142163400-142165000	Weak transcription	Right Ventricle	heart
11	chr3:142163400-142165800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:142163400-142166000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:142163400-142166000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:142163400-142166000	Weak transcription	Lung	lung
15	chr3:142163600-142166000	Weak transcription	Pancreas	Pancrea
16	chr3:142164000-142165200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:142164000-142165600	Enhancers	Fetal Brain Male	brain
18	chr3:142164000-142165800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:142164200-142165000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr3:142164200-142165000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:142164200-142165200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:142164200-142165400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:142164200-142166000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:142164200-142166000	Flanking Active TSS	Dnd41	blood
25	chr3:142164200-142166200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr3:142164200-142166200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:142164400-142165000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr3:142164400-142165000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:142164400-142165000	Flanking Active TSS	HepG2	liver
30	chr3:142164400-142165200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:142164400-142165200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:142164400-142165400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:142164400-142165400	Enhancers	Aorta	Aorta
34	chr3:142164400-142165400	Flanking Active TSS	Liver	Liver
35	chr3:142164400-142165400	Enhancers	Brain Angular Gyrus	brain
36	chr3:142164400-142165400	Enhancers	Brain Substantia Nigra	brain
37	chr3:142164400-142165400	Enhancers	Colon Smooth Muscle	Colon
38	chr3:142164400-142165400	Enhancers	A549	lung
39	chr3:142164400-142165600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:142164400-142165600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr3:142164400-142165600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr3:142164400-142165600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:142164400-142165600	Flanking Active TSS	Osteobl	bone
44	chr3:142164400-142165800	Enhancers	Primary B cells from peripheral blood	blood
45	chr3:142164400-142165800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr3:142164400-142166000	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr3:142164400-142166000	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr3:142164400-142166000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:142164400-142166000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:142164400-142166200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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