Variant report

Variant	rs542506089
Chromosome Location	chr5:98263755-98263756
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	chr5:98263639-98265621	HEK293	kidney:	n/a	n/a
2	STAT1	chr5:98263562-98265931	Hela-S3	cervix:	n/a	chr5:98264812-98264824 chr5:98264209-98264221 chr5:98264684-98264696 chr5:98264816-98264828 chr5:98263883-98263895
3	JUND	chr5:98263604-98266054	K562	blood:	n/a	chr5:98264819-98264828 chr5:98264814-98264823 chr5:98264709-98264718 chr5:98264752-98264761 chr5:98263844-98263853 chr5:98263774-98263783 chr5:98264219-98264228 chr5:98264818-98264827
4	MTA3	chr5:98262831-98263840	GM12878	blood:	n/a	n/a
5	E2F6	chr5:98263557-98264082	H1-hESC	embryonic stem cell:	n/a	chr5:98263874-98263884 chr5:98263818-98263830
6	POLR2A	chr5:98263028-98265628	Raji	blood:	n/a	n/a
7	CHD2	chr5:98263622-98264062	HepG2	liver:	n/a	chr5:98263846-98263856
8	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
9	MXI1	chr5:98262891-98265927	GM12878	blood:	n/a	n/a
10	MAX	chr5:98263606-98265737	Hela-S3	cervix:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
11	MAX	chr5:98263427-98264253	ECC-1	luminal epithelium:	n/a	chr5:98263904-98263911 chr5:98263903-98263912 chr5:98263849-98263859 chr5:98263901-98263916
12	POLR2A	chr5:98263634-98265573	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr5:98262735-98265849	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:98262939-98265984	GM19193	blood:	n/a	n/a
15	POLR2A	chr5:98263688-98263839	A549	lung:	n/a	n/a
16	RCOR1	chr5:98263448-98263758	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:98262882-98265836	GM12891	blood:	n/a	n/a
18	POLR2A	chr5:98262425-98264148	A549	lung:	n/a	n/a
19	POLR2A	chr5:98262881-98266666	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:98262884-98263828	GM12891	blood:	n/a	n/a
21	POLR2A	chr5:98262834-98263841	GM12878	blood:	n/a	n/a
22	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
23	MYC	chr5:98263748-98266144	MCF10A-Er-Src	breast:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
24	TCF7L2	chr5:98263628-98265600	HCT-116	colon:	n/a	n/a
25	TBP	chr5:98263655-98264117	H1-hESC	embryonic stem cell:	n/a	n/a
26	SIN3AK20	chr5:98263424-98265879	MCF-7	breast:	n/a	n/a
27	E2F6	chr5:98263511-98264105	A549	lung:	n/a	chr5:98263874-98263884 chr5:98263818-98263830
28	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
29	POLR2A	chr5:98262802-98266065	GM12878	blood:	n/a	n/a
30	MAX	chr5:98263519-98265643	A549	lung:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
31	POLR2A	chr5:98262863-98266842	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:98263708-98265658	MCF-7	breast:	n/a	n/a
33	POLR2A	chr5:98262881-98266708	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:98263568-98265943	K562	blood:	n/a	n/a
35	POLR2A	chr5:98262788-98265865	GM12892	blood:	n/a	n/a
36	MXI1	chr5:98263602-98264117	H1-hESC	embryonic stem cell:	n/a	n/a
37	CREB1	chr5:98263608-98265745	HepG2	liver:	n/a	n/a
38	POLR2A	chr5:98262824-98265848	GM12892	blood:	n/a	n/a
39	MAX	chr5:98263633-98264240	H1-hESC	embryonic stem cell:	n/a	chr5:98263904-98263911 chr5:98263903-98263912 chr5:98263849-98263859 chr5:98263901-98263916
40	HEY1	chr5:98263388-98263825	K562	blood:	n/a	n/a
41	POLR2A	chr5:98262736-98267954	MCF10A-Er-Src	breast:	n/a	n/a
42	RCOR1	chr5:98262909-98265682	K562	blood:	n/a	n/a
43	MYC	chr5:98263755-98264050	HepG2	liver:	n/a	chr5:98263904-98263911 chr5:98263903-98263912 chr5:98263849-98263859 chr5:98263901-98263916
44	CHD2	chr5:98263675-98265627	Hela-S3	cervix:	n/a	chr5:98263846-98263856 chr5:98264811-98264821 chr5:98264740-98264750
45	POLR2A	chr5:98263461-98263878	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr5:98263643-98265661	H1-neurons	neurons:	n/a	n/a
47	POLR2A	chr5:98263627-98266694	K562	blood:	n/a	n/a
48	USF1	chr5:98263733-98264104	ECC-1	luminal epithelium:	n/a	n/a
49	MYC	chr5:98263642-98265656	Hela-S3	cervix:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
50	HA-E2F1	chr5:98263520-98265951	MCF-7	breast:	n/a	chr5:98263874-98263884 chr5:98264753-98264765 chr5:98264222-98264231 chr5:98263818-98263830 chr5:98265228-98265238 chr5:98264836-98264845

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:98263747-98263797	HIPEpiC	eye:	n/a
2	chr5:98263747-98263797	AG09319	gingival:	n/a
3	chr5:98263747-98263797	AG04450	lung:	fetal
4	chr5:98263747-98263797	SK-N-SH_RA	brain:	n/a
5	chr5:98263747-98263797	ProgFib	skin:	n/a
6	chr5:98263747-98263797	Hepatocyte	liver:	n/a
7	chr5:98263747-98263797	HEEpiC	esophagus:	n/a
8	chr5:98263747-98263797	HCT-116	colon:	n/a
9	chr5:98263747-98263797	HMEC	breast:	n/a
10	chr5:98263747-98263797	HRCEpiC	kidney:	n/a
11	chr5:98263747-98263797	T-47D	breast:	n/a
12	chr5:98263747-98263797	PFSK-1	brain:	n/a
13	chr5:98263747-98263797	K562	blood:	n/a
14	chr5:98263747-98263797	HCF	heart:	n/a
15	chr5:98263747-98263797	LNCaP	prostate:	n/a
16	chr5:98263747-98263797	SK-N-SH	brain:	n/a
17	chr5:98263747-98263797	GM19239	blood:	n/a
18	chr5:98263747-98263797	HL-60	blood:	n/a
19	chr5:98263747-98263797	PANC-1	pancreas:	n/a
20	chr5:98263747-98263797	SK-N-MC	brain:	n/a
21	chr5:98263747-98263797	AG10803	skin:	n/a
22	chr5:98263747-98263797	NB4	blood:	n/a
23	chr5:98263747-98263797	NHDF-neo	bronchial:	n/a
24	chr5:98263747-98263797	U87	brain:	n/a
25	chr5:98263747-98263797	HPAEpiC	pulmonary alveolar:	n/a
26	chr5:98263747-98263797	GM06990	blood:	n/a
27	chr5:98263747-98263797	HRPEpiC	eye:	n/a
28	chr5:98263747-98263797	MCF-7	breast:	n/a
29	chr5:98263747-98263797	HRE	kidney:	n/a
30	chr5:98263747-98263797	RPTEC	kidney:	n/a
31	chr5:98263747-98263797	Caco-2	colon:	n/a
32	chr5:98263747-98263797	HEK293	kidney:	embryo
33	chr5:98263747-98263797	Jurkat	blood:	n/a
34	chr5:98263747-98263797	PrEC	prostate:	n/a
35	chr5:98263747-98263797	BJ	skin:	n/a
36	chr5:98263747-98263797	HepG2	liver:	n/a
37	chr5:98263747-98263797	BE2_C	brain:	n/a
38	chr5:98263747-98263797	SKMC	muscle:	n/a
39	chr5:98263747-98263797	HNPCEpiC	eye:	n/a
40	chr5:98263747-98263797	ECC-1	luminal epithelium:	n/a
41	chr5:98263747-98263797	NHBE	bronchial:	n/a
42	chr5:98263747-98263797	IMR90	lung:	fetal
43	chr5:98263747-98263797	HUVEC	blood vessel:	n/a
44	chr5:98263747-98263797	A549	lung:	n/a
45	chr5:98263747-98263797	CMK	blood:	n/a
46	chr5:98263747-98263797	AG04449	skin:	fetal
47	chr5:98263747-98263797	GM12891	blood:	n/a
48	chr5:98263747-98263797	HCM	heart:	n/a
49	chr5:98263747-98263797	NT2-D1	testis:	n/a
50	chr5:98263747-98263797	NH-A	brain:	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:
10	chr5:98204205..98207501-chr5:98263457..98266267,3	MCF-7	breast:

Variant related genes	Relation type
CHD1	TF binding region
ENSG00000248489	TF binding region
CHD1	CpG island
ENSG00000248489	CpG island
ENSG00000200351	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000241597	Chromatin interaction
ENSG00000153922	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	chr5:98261200-98266000	Active TSS	Thymus	Thymus
2	chr5:98261600-98265800	Active TSS	GM12878-XiMat	blood
3	chr5:98261600-98266200	Active TSS	Fetal Thymus	thymus
4	chr5:98261800-98266200	Active TSS	K562	blood
5	chr5:98262000-98266000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:98262000-98266000	Active TSS	A549	lung
7	chr5:98262200-98263800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr5:98262200-98263800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:98262200-98265600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr5:98262200-98265800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:98262200-98265800	Active TSS	HMEC	breast
12	chr5:98262200-98266000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:98262400-98264600	Active TSS	Right Atrium	heart
14	chr5:98262400-98265800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:98262400-98266000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:98262400-98266000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr5:98262400-98266000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr5:98262400-98266000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:98262400-98266200	Active TSS	Right Ventricle	heart
20	chr5:98262600-98263800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr5:98262600-98263800	Flanking Active TSS	Liver	Liver
22	chr5:98262600-98265000	Active TSS	Brain Germinal Matrix	brain
23	chr5:98262600-98265600	Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr5:98262600-98265800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:98262600-98265800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:98262600-98265800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:98262600-98265800	Active TSS	Fetal Intestine Small	intestine
28	chr5:98262600-98266000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:98262600-98266000	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr5:98262600-98266000	Active TSS	Colon Smooth Muscle	Colon
31	chr5:98262600-98266000	Active TSS	Fetal Intestine Large	intestine
32	chr5:98262600-98266000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr5:98262600-98266000	Active TSS	HSMM	muscle
34	chr5:98262600-98266200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr5:98262600-98266200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:98262600-98266200	Active TSS	NHLF	lung
37	chr5:98262600-98266400	Active TSS	Psoas Muscle	Psoas
38	chr5:98262600-98266600	Active TSS	Stomach Smooth Muscle	stomach
39	chr5:98262600-98266800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:98262800-98264000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:98262800-98264600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:98262800-98265800	Active TSS	Primary monocytes fromperipheralblood	blood
43	chr5:98262800-98265800	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr5:98262800-98265800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:98262800-98265800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr5:98262800-98265800	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr5:98262800-98265800	Active TSS	Fetal Muscle Trunk	muscle
48	chr5:98262800-98266000	Active TSS	H9 Cell Line	embryonic stem cell
49	chr5:98262800-98266000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:98262800-98266000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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