Variant report

Variant	rs560872009
Chromosome Location	chr5:98264314-98264315
allele	C/T
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	RELA	chr5:98264123-98265685	GM18951	blood:	n/a	n/a
5	POLR2A	chr5:98263028-98265628	Raji	blood:	n/a	n/a
6	TAF1	chr5:98264247-98265633	SK-N-SH	brain:	n/a	n/a
7	E2F4	chr5:98264300-98265664	MCF10A-Er-Src	breast:	n/a	chr5:98264754-98264765 chr5:98264753-98264765 chr5:98265228-98265238 chr5:98264836-98264845
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	POLR2A	chr5:98263634-98265573	HUVEC	blood vessel:	n/a	n/a
12	ZBTB7A	chr5:98264265-98264452	K562	blood:	n/a	n/a
13	POLR2A	chr5:98262735-98265849	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:98263793-98265554	HepG2	liver:	n/a	n/a
15	POLR2A	chr5:98262939-98265984	GM19193	blood:	n/a	n/a
16	POLR2A	chr5:98264252-98265628	HUVEC	blood vessel:	n/a	n/a
17	CREB1	chr5:98264205-98265697	K562	blood:	n/a	n/a
18	ELF1	chr5:98263781-98265592	GM12878	blood:	n/a	chr5:98264044-98264056 chr5:98265478-98265490 chr5:98264808-98264820
19	YY1	chr5:98263759-98265562	K562	blood:	n/a	chr5:98264225-98264234 chr5:98263876-98263885 chr5:98264818-98264827 chr5:98263874-98263888 chr5:98264222-98264231 chr5:98265092-98265103 chr5:98264816-98264827 chr5:98264567-98264578 chr5:98264219-98264230
20	TAL1	chr5:98264165-98265632	K562	blood:	n/a	chr5:98264556-98264574
21	POLR2A	chr5:98263876-98264444	A549	lung:	n/a	n/a
22	RAD21	chr5:98264263-98264334	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:98262882-98265836	GM12891	blood:	n/a	n/a
24	RELA	chr5:98264104-98265602	GM19099	blood:	n/a	n/a
25	POLR2A	chr5:98262881-98266666	HepG2	liver:	n/a	n/a
26	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
27	BCLAF1	chr5:98264244-98265731	GM12878	blood:	n/a	chr5:98264816-98264825 chr5:98264256-98264265 chr5:98264399-98264408 chr5:98265227-98265240 chr5:98264814-98264827
28	MAX	chr5:98264264-98265591	H1-hESC	embryonic stem cell:	n/a	chr5:98264544-98264554 chr5:98264754-98264764
29	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
30	TCF7L2	chr5:98263628-98265600	HCT-116	colon:	n/a	n/a
31	EGR1	chr5:98264192-98265889	HCT-116	colon:	n/a	chr5:98264836-98264845 chr5:98265424-98265438 chr5:98264835-98264844 chr5:98264818-98264828 chr5:98265225-98265238 chr5:98265480-98265490 chr5:98264819-98264832 chr5:98265424-98265435 chr5:98264226-98264239 chr5:98264362-98264372 chr5:98265087-98265100 chr5:98264709-98264719 chr5:98264721-98264730 chr5:98264509-98264523 chr5:98265324-98265348 chr5:98264360-98264373 chr5:98264285-98264298 chr5:98264541-98264555
32	SIN3AK20	chr5:98263424-98265879	MCF-7	breast:	n/a	n/a
33	GABPA	chr5:98264314-98265595	K562	blood:	n/a	chr5:98264835-98264844 chr5:98264835-98264849 chr5:98264832-98264846 chr5:98264835-98264846
34	POLR2A	chr5:98263828-98265673	K562	blood:	n/a	n/a
35	PAX5	chr5:98264297-98265572	GM12878	blood:	n/a	chr5:98265301-98265320 chr5:98264836-98264845 chr5:98264535-98264544 chr5:98264589-98264608 chr5:98264714-98264723
36	POLR2A	chr5:98263835-98265551	A549	lung:	n/a	n/a
37	POLR2A	chr5:98264280-98265764	GM12891	blood:	n/a	n/a
38	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
39	RUNX3	chr5:98264206-98265644	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:98262802-98266065	GM12878	blood:	n/a	n/a
41	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
42	JUND	chr5:98263928-98265679	A549	lung:	n/a	chr5:98264819-98264828 chr5:98264814-98264823 chr5:98264709-98264718 chr5:98264752-98264761 chr5:98264219-98264228 chr5:98264818-98264827
43	POLR2A	chr5:98262863-98266842	GM12878	blood:	n/a	n/a
44	POLR2A	chr5:98263708-98265658	MCF-7	breast:	n/a	n/a
45	POLR2A	chr5:98262881-98266708	GM12878	blood:	n/a	n/a
46	POLR2A	chr5:98263568-98265943	K562	blood:	n/a	n/a
47	POLR2A	chr5:98262788-98265865	GM12892	blood:	n/a	n/a
48	TAF1	chr5:98264292-98265636	MCF-7	breast:	n/a	n/a
49	CREB1	chr5:98263608-98265745	HepG2	liver:	n/a	n/a
50	POLR2A	chr5:98262824-98265848	GM12892	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:98264283-98264333	T-47D	breast:	n/a
2	chr5:98264283-98264333	HEK293	kidney:	embryo
3	chr5:98264283-98264333	Hepatocyte	liver:	n/a
4	chr5:98264283-98264333	A549	lung:	n/a
5	chr5:98264283-98264333	GM12878	blood:	n/a
6	chr5:98264283-98264333	NHBE	bronchial:	n/a
7	chr5:98264283-98264333	GM12891	blood:	n/a
8	chr5:98264283-98264333	K562	blood:	n/a
9	chr5:98264283-98264333	BE2_C	brain:	n/a
10	chr5:98264283-98264333	ProgFib	skin:	n/a
11	chr5:98264283-98264333	HRPEpiC	eye:	n/a
12	chr5:98264283-98264333	HCT-116	colon:	n/a
13	chr5:98264283-98264333	SK-N-MC	brain:	n/a
14	chr5:98264283-98264333	Hela-S3	cervix:	n/a
15	chr5:98264283-98264333	CMK	blood:	n/a
16	chr5:98264283-98264333	HCPEpiC	choroid plexus:	n/a
17	chr5:98264283-98264333	HUVEC	blood vessel:	n/a
18	chr5:98264283-98264333	HPAEpiC	pulmonary alveolar:	n/a
19	chr5:98264283-98264333	H1-hESC	embryonic stem cell:	embryo
20	chr5:98264283-98264333	NH-A	brain:	n/a
21	chr5:98264283-98264333	BJ	skin:	n/a
22	chr5:98264283-98264333	HepG2	liver:	n/a
23	chr5:98264283-98264333	PFSK-1	brain:	n/a
24	chr5:98264283-98264333	HAEpiC	amniotic membrane:	n/a
25	chr5:98264283-98264333	HIPEpiC	eye:	n/a
26	chr5:98264283-98264333	MCF-7	breast:	n/a
27	chr5:98264283-98264333	IMR90	lung:	fetal
28	chr5:98264283-98264333	HCM	heart:	n/a
29	chr5:98264283-98264333	HRE	kidney:	n/a
30	chr5:98264283-98264333	Jurkat	blood:	n/a
31	chr5:98264283-98264333	RPTEC	kidney:	n/a
32	chr5:98264283-98264333	HL-60	blood:	n/a
33	chr5:98264283-98264333	ovcar-3	ovarian:	n/a
34	chr5:98264283-98264333	PANC-1	pancreas:	n/a
35	chr5:98264283-98264333	MCF10A-Er-Src	breast:	n/a
36	chr5:98264283-98264333	GM06990	blood:	n/a
37	chr5:98264283-98264333	GM12892	blood:	n/a
38	chr5:98264283-98264333	SK-N-SH	brain:	n/a
39	chr5:98264283-98264333	AG09309	skin:	n/a
40	chr5:98264283-98264333	NB4	blood:	n/a
41	chr5:98264283-98264333	GM19239	blood:	n/a
42	chr5:98264283-98264333	U87	brain:	n/a
43	chr5:98264283-98264333	NT2-D1	testis:	n/a
44	chr5:98264283-98264333	AG09319	gingival:	n/a
45	chr5:98264283-98264333	SKMC	muscle:	n/a
46	chr5:98264283-98264333	HNPCEpiC	eye:	n/a
47	chr5:98264283-98264333	AG04449	skin:	fetal
48	chr5:98264283-98264333	Caco-2	colon:	n/a
49	chr5:98264283-98264333	AG10803	skin:	n/a
50	chr5:98264283-98264333	AoSMC	blood vessel:	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	chr3:48487968..48488563-chr5:98263988..98264982,2	Hela-S3	cervix:
6	chr5:98262538..98264376-chr5:98385068..98386574,2	K562	blood:
7	chr5:98264226..98265182-chr7:66093354..66094059,2	Hela-S3	cervix:
8	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
9	chr12:46120952..46121817-chr5:98263968..98264550,2	HCT-116	colon:
10	chr5:98220809..98224769-chr5:98261722..98266325,5	K562	blood:
11	chr1:154946397..154946999-chr5:98264263..98264810,2	Hela-S3	cervix:
12	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:
13	chr5:90674940..90677586-chr5:98263946..98266440,2	K562	blood:
14	chr15:83478349..83478996-chr5:98264221..98265198,2	Hela-S3	cervix:
15	chr19:12845070..12845760-chr5:98264143..98265041,2	Hela-S3	cervix:
16	chr5:98237133..98240076-chr5:98262664..98264455,2	K562	blood:
17	chr5:98204205..98207501-chr5:98263457..98266267,3	MCF-7	breast:
18	chr5:98263971..98264737-chr7:120590626..120591131,2	Hela-S3	cervix:

Variant related genes	Relation type
CHD1	TF binding region
ENSG00000248489	TF binding region
CHD1	CpG island
ENSG00000248489	CpG island
ENSG00000273015	Chromatin interaction
ENSG00000200351	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000071243	Chromatin interaction
ENSG00000153922	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000123144	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000241597	Chromatin interaction
ENSG00000244380	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	chr5:98262200-98265600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:98262200-98265800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:98262200-98265800	Active TSS	HMEC	breast
10	chr5:98262200-98266000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:98262400-98264600	Active TSS	Right Atrium	heart
12	chr5:98262400-98265800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:98262400-98266000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr5:98262400-98266000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr5:98262400-98266000	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr5:98262400-98266000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:98262400-98266200	Active TSS	Right Ventricle	heart
18	chr5:98262600-98265000	Active TSS	Brain Germinal Matrix	brain
19	chr5:98262600-98265600	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr5:98262600-98265800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:98262600-98265800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:98262600-98265800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:98262600-98265800	Active TSS	Fetal Intestine Small	intestine
24	chr5:98262600-98266000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:98262600-98266000	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:98262600-98266000	Active TSS	Colon Smooth Muscle	Colon
27	chr5:98262600-98266000	Active TSS	Fetal Intestine Large	intestine
28	chr5:98262600-98266000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr5:98262600-98266000	Active TSS	HSMM	muscle
30	chr5:98262600-98266200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr5:98262600-98266200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:98262600-98266200	Active TSS	NHLF	lung
33	chr5:98262600-98266400	Active TSS	Psoas Muscle	Psoas
34	chr5:98262600-98266600	Active TSS	Stomach Smooth Muscle	stomach
35	chr5:98262600-98266800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:98262800-98264600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:98262800-98265800	Active TSS	Primary monocytes fromperipheralblood	blood
38	chr5:98262800-98265800	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr5:98262800-98265800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:98262800-98265800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr5:98262800-98265800	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr5:98262800-98265800	Active TSS	Fetal Muscle Trunk	muscle
43	chr5:98262800-98266000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr5:98262800-98266000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:98262800-98266000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:98262800-98266000	Active TSS	Fetal Kidney	kidney
47	chr5:98262800-98266200	Active TSS	Fetal Stomach	stomach
48	chr5:98262800-98266200	Active TSS	HSMMtube	muscle
49	chr5:98262800-98266200	Active TSS	NHDF-Ad	bronchial
50	chr5:98263000-98265400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

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