Variant report

Variant	rs542404797
Chromosome Location	chr5:98263442-98263443
allele	-/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	MTA3	chr5:98262831-98263840	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:98263028-98265628	Raji	blood:	n/a	n/a
3	MAZ	chr5:98262858-98265677	K562	blood:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
4	MXI1	chr5:98262891-98265927	GM12878	blood:	n/a	n/a
5	MAX	chr5:98263427-98264253	ECC-1	luminal epithelium:	n/a	chr5:98263904-98263911 chr5:98263903-98263912 chr5:98263849-98263859 chr5:98263901-98263916
6	POLR2A	chr5:98262735-98265849	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr5:98262939-98265984	GM19193	blood:	n/a	n/a
8	POLR2A	chr5:98262882-98265836	GM12891	blood:	n/a	n/a
9	POLR2A	chr5:98262425-98264148	A549	lung:	n/a	n/a
10	POLR2A	chr5:98262881-98266666	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:98262884-98263828	GM12891	blood:	n/a	n/a
12	POLR2A	chr5:98262834-98263841	GM12878	blood:	n/a	n/a
13	GTF2F1	chr5:98262931-98263607	Hela-S3	cervix:	n/a	n/a
14	MAX	chr5:98262962-98265658	NB4	blood:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
15	SIN3AK20	chr5:98263424-98265879	MCF-7	breast:	n/a	n/a
16	CUX1	chr5:98262820-98263496	GM12878	blood:	n/a	n/a
17	MYC	chr5:98262962-98265649	NB4	blood:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
18	POLR2A	chr5:98262802-98266065	GM12878	blood:	n/a	n/a
19	RAD21	chr5:98263418-98263701	A549	lung:	n/a	n/a
20	POLR2A	chr5:98262863-98266842	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:98262881-98266708	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:98262788-98265865	GM12892	blood:	n/a	n/a
23	POLR2A	chr5:98262824-98265848	GM12892	blood:	n/a	n/a
24	POLR2A	chr5:98263440-98263516	ProgFib	skin:	n/a	n/a
25	GABPA	chr5:98262667-98263500	MCF-7	breast:	n/a	n/a
26	HEY1	chr5:98263388-98263825	K562	blood:	n/a	n/a
27	POLR2A	chr5:98262736-98267954	MCF10A-Er-Src	breast:	n/a	n/a
28	RCOR1	chr5:98262909-98265682	K562	blood:	n/a	n/a
29	IRF1	chr5:98262843-98263461	K562	blood:	n/a	n/a
30	POLR2A	chr5:98261911-98271717	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr5:98262744-98270017	GM12891	blood:	n/a	n/a
32	SIN3A	chr5:98263421-98264661	GM12878	blood:	n/a	chr5:98264565-98264578
33	STAT5A	chr5:98262861-98263748	GM12878	blood:	n/a	chr5:98263044-98263056 chr5:98263164-98263171 chr5:98263370-98263381
34	POLR2A	chr5:98262705-98266805	PBDE	blood:	n/a	n/a
35	ATF2	chr5:98262812-98263803	GM12878	blood:	n/a	chr5:98262913-98262920
36	POLR2A	chr5:98262866-98263864	GM12892	blood:	n/a	n/a
37	POLR2A	chr5:98262041-98266821	IMR90	lung:	n/a	n/a
38	UBTF	chr5:98262938-98265596	K562	blood:	n/a	n/a
39	POLR2A	chr5:98262821-98264060	U87	brain:	n/a	n/a
40	POLR2A	chr5:98262918-98263848	GM12891	blood:	n/a	n/a
41	POLR2A	chr5:98262950-98265882	Hela-S3	cervix:	n/a	n/a
42	RELA	chr5:98262918-98263791	GM12891	blood:	n/a	n/a
43	CHD2	chr5:98262960-98265678	GM12878	blood:	n/a	chr5:98263846-98263856 chr5:98264811-98264821 chr5:98264740-98264750
44	POLR2A	chr5:98263438-98265553	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAZ	chr5:98262674-98263567	GM12878	blood:	n/a	n/a
46	RFX5	chr5:98262961-98263710	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr5:98262906-98266708	K562	blood:	n/a	n/a
48	ZMIZ1	chr5:98262797-98263570	K562	blood:	n/a	n/a
49	POLR2A	chr5:98262919-98266641	GM12892	blood:	n/a	n/a
50	POLR2A	chr5:98262745-98263490	HUVEC	blood vessel:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:98263417-98263467	CMK	blood:	n/a
2	chr5:98263417-98263467	HRE	kidney:	n/a
3	chr5:98263417-98263467	RPTEC	kidney:	n/a
4	chr5:98263417-98263467	HRCEpiC	kidney:	n/a
5	chr5:98263417-98263467	HRPEpiC	eye:	n/a
6	chr5:98263417-98263467	HMEC	breast:	n/a
7	chr5:98263417-98263467	Jurkat	blood:	n/a
8	chr5:98263417-98263467	AG04449	skin:	fetal
9	chr5:98263417-98263467	AG10803	skin:	n/a
10	chr5:98263417-98263467	GM06990	blood:	n/a
11	chr5:98263417-98263467	GM19239	blood:	n/a
12	chr5:98263417-98263467	PANC-1	pancreas:	n/a
13	chr5:98263417-98263467	SK-N-MC	brain:	n/a
14	chr5:98263417-98263467	AoSMC	blood vessel:	n/a
15	chr5:98263417-98263467	PFSK-1	brain:	n/a
16	chr5:98263417-98263467	ECC-1	luminal epithelium:	n/a
17	chr5:98263417-98263467	AG09309	skin:	n/a
18	chr5:98263417-98263467	BJ	skin:	n/a
19	chr5:98263417-98263467	MCF-7	breast:	n/a
20	chr5:98263417-98263467	HUVEC	blood vessel:	n/a
21	chr5:98263417-98263467	NT2-D1	testis:	n/a
22	chr5:98263417-98263467	AG04450	lung:	fetal
23	chr5:98263417-98263467	NHBE	bronchial:	n/a
24	chr5:98263417-98263467	Caco-2	colon:	n/a
25	chr5:98263417-98263467	GM12891	blood:	n/a
26	chr5:98263417-98263467	HNPCEpiC	eye:	n/a
27	chr5:98263417-98263467	MCF10A-Er-Src	breast:	n/a
28	chr5:98263417-98263467	IMR90	lung:	fetal
29	chr5:98263417-98263467	ProgFib	skin:	n/a
30	chr5:98263417-98263467	BE2_C	brain:	n/a
31	chr5:98263417-98263467	A549	lung:	n/a
32	chr5:98263417-98263467	HPAEpiC	pulmonary alveolar:	n/a
33	chr5:98263417-98263467	SK-N-SH_RA	brain:	n/a
34	chr5:98263417-98263467	HAEpiC	amniotic membrane:	n/a
35	chr5:98263417-98263467	T-47D	breast:	n/a
36	chr5:98263417-98263467	Hepatocyte	liver:	n/a
37	chr5:98263417-98263467	SK-N-SH	brain:	n/a
38	chr5:98263417-98263467	HEK293	kidney:	embryo
39	chr5:98263417-98263467	SKMC	muscle:	n/a
40	chr5:98263417-98263467	NHDF-neo	bronchial:	n/a
41	chr5:98263417-98263467	HL-60	blood:	n/a
42	chr5:98263417-98263467	H1-hESC	embryonic stem cell:	embryo
43	chr5:98263417-98263467	NH-A	brain:	n/a
44	chr5:98263417-98263467	HCT-116	colon:	n/a
45	chr5:98263417-98263467	GM12878	blood:	n/a
46	chr5:98263417-98263467	AG09319	gingival:	n/a
47	chr5:98263417-98263467	SAEC	small airway:	n/a
48	chr5:98263417-98263467	NB4	blood:	n/a
49	chr5:98263417-98263467	HIPEpiC	eye:	n/a
50	chr5:98263417-98263467	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:98262437..98267686-chr5:98287585..98292205,9	K562	blood:
2	chr5:98263162..98264704-chr5:98365544..98368385,2	K562	blood:
3	chr5:98220770..98224200-chr5:98262773..98266161,4	K562	blood:
4	chr5:90674940..90679357-chr5:98262514..98267275,7	K562	blood:
5	chr5:98262538..98264376-chr5:98385068..98386574,2	K562	blood:
6	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
7	chr5:98220809..98224769-chr5:98261722..98266325,5	K562	blood:
8	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:
9	chr5:98237133..98240076-chr5:98262664..98264455,2	K562	blood:

Variant related genes	Relation type
CHD1	TF binding region
ENSG00000248489	TF binding region
CHD1	CpG island
ENSG00000248489	CpG island
ENSG00000153922	Chromatin interaction
ENSG00000200351	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000241597	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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3405878	chr5:98263077-98265925	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	esv3346760	chr5:98263202-98265950	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 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	chr5:98260000-98263600	Weak transcription	Spleen	Spleen
2	chr5:98261200-98266000	Active TSS	Thymus	Thymus
3	chr5:98261600-98265800	Active TSS	GM12878-XiMat	blood
4	chr5:98261600-98266200	Active TSS	Fetal Thymus	thymus
5	chr5:98261800-98266200	Active TSS	K562	blood
6	chr5:98262000-98266000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:98262000-98266000	Active TSS	A549	lung
8	chr5:98262200-98263600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:98262200-98263800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr5:98262200-98263800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:98262200-98265600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr5:98262200-98265800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:98262200-98265800	Active TSS	HMEC	breast
14	chr5:98262200-98266000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr5:98262400-98263600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:98262400-98263600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:98262400-98264600	Active TSS	Right Atrium	heart
18	chr5:98262400-98265800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:98262400-98266000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr5:98262400-98266000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr5:98262400-98266000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr5:98262400-98266000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:98262400-98266200	Active TSS	Right Ventricle	heart
24	chr5:98262600-98263600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr5:98262600-98263800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr5:98262600-98263800	Flanking Active TSS	Liver	Liver
27	chr5:98262600-98265000	Active TSS	Brain Germinal Matrix	brain
28	chr5:98262600-98265600	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr5:98262600-98265800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:98262600-98265800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:98262600-98265800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:98262600-98265800	Active TSS	Fetal Intestine Small	intestine
33	chr5:98262600-98266000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:98262600-98266000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr5:98262600-98266000	Active TSS	Colon Smooth Muscle	Colon
36	chr5:98262600-98266000	Active TSS	Fetal Intestine Large	intestine
37	chr5:98262600-98266000	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr5:98262600-98266000	Active TSS	HSMM	muscle
39	chr5:98262600-98266200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr5:98262600-98266200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:98262600-98266200	Active TSS	NHLF	lung
42	chr5:98262600-98266400	Active TSS	Psoas Muscle	Psoas
43	chr5:98262600-98266600	Active TSS	Stomach Smooth Muscle	stomach
44	chr5:98262600-98266800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:98262800-98263600	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr5:98262800-98263600	Flanking Active TSS	Fetal Lung	lung
47	chr5:98262800-98264000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:98262800-98264600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:98262800-98265800	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr5:98262800-98265800	Active TSS	Primary T helper naive cells from peripheral blood	blood

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