Variant report

Variant	rs556593554
Chromosome Location	chr1:158980086-158980087
allele	A/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	BCLAF1	chr1:158979353-158980167	GM12878	blood:	n/a	chr1:158979355-158979364
2	STAT3	chr1:158978735-158980510	MCF10A-Er-Src	breast:	n/a	chr1:158979842-158979853 chr1:158979355-158979364
3	FOS	chr1:158979336-158980577	MCF10A-Er-Src	breast:	n/a	chr1:158979356-158979363 chr1:158980113-158980122 chr1:158979356-158979365 chr1:158980385-158980394
4	CCNT2	chr1:158979674-158980235	K562	blood:	n/a	n/a
5	POLR2A	chr1:158978406-158980376	GM12892	blood:	n/a	n/a
6	TBP	chr1:158978436-158980668	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:158978455-158980617	GM18951	blood:	n/a	n/a
8	FOS	chr1:158979127-158980621	MCF10A-Er-Src	breast:	n/a	chr1:158979356-158979363 chr1:158980113-158980122 chr1:158979356-158979365 chr1:158980385-158980394
9	POLR2A	chr1:158978428-158980356	GM12892	blood:	n/a	n/a
10	KAP1	chr1:158978548-158980551	HEK293	kidney:	n/a	chr1:158979354-158979363
11	CEBPB	chr1:158979315-158980401	IMR90	lung:	n/a	n/a
12	STAT2	chr1:158979402-158980141	K562	blood:	n/a	chr1:158979640-158979655
13	FOS	chr1:158979119-158980165	MCF10A-Er-Src	breast:	n/a	chr1:158979356-158979363 chr1:158980113-158980122 chr1:158979356-158979365
14	IKZF1	chr1:158979567-158980134	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:158979432-158980288	HUVEC	blood vessel:	n/a	n/a
16	NFYA	chr1:158979984-158980174	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:158978508-158980689	GM12892	blood:	n/a	n/a
18	EP300	chr1:158979423-158980722	Hela-S3	cervix:	n/a	chr1:158980664-158980674
19	POLR2A	chr1:158978461-158980586	GM18526	blood:	n/a	n/a
20	EP300	chr1:158979512-158980152	K562	blood:	n/a	n/a
21	CUX1	chr1:158979375-158980175	GM12878	blood:	n/a	n/a
22	MXI1	chr1:158978956-158981134	IMR90	lung:	n/a	n/a
23	POLR2A	chr1:158978459-158981042	GM15510	blood:	n/a	n/a
24	STAT5A	chr1:158979556-158980115	K562	blood:	n/a	n/a
25	KAP1	chr1:158978346-158980205	U2OS	brain:	n/a	chr1:158979354-158979363
26	GTF2F1	chr1:158979204-158980177	Hela-S3	cervix:	n/a	n/a
27	GATA2	chr1:158979561-158980192	HUVEC	blood vessel:	n/a	chr1:158979774-158979788
28	RCOR1	chr1:158978512-158980241	GM12878	blood:	n/a	n/a
29	BRCA1	chr1:158979337-158980558	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:158979131-158980643	U87	brain:	n/a	n/a
31	STAT3	chr1:158978935-158980925	MCF10A-Er-Src	breast:	n/a	chr1:158979842-158979853 chr1:158979355-158979364
32	USF2	chr1:158979480-158980200	Hela-S3	cervix:	n/a	n/a
33	MAX	chr1:158979360-158980636	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr1:158978710-158981534	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr1:158979144-158980622	MCF10A-Er-Src	breast:	n/a	chr1:158979356-158979363 chr1:158980113-158980122 chr1:158979356-158979365 chr1:158980385-158980394
36	STAT3	chr1:158978936-158980665	MCF10A-Er-Src	breast:	n/a	chr1:158979842-158979853 chr1:158979355-158979364
37	STAT3	chr1:158979293-158980479	Hela-S3	cervix:	n/a	chr1:158979842-158979853 chr1:158979355-158979364
38	POLR2A	chr1:158978457-158980760	GM12878	blood:	n/a	n/a
39	GATA3	chr1:158979296-158980414	SK-N-SH	brain:	n/a	n/a
40	TBL1XR1	chr1:158979242-158980155	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:158978464-158986840	GM12892	blood:	n/a	n/a
42	RCOR1	chr1:158979338-158980201	K562	blood:	n/a	n/a
43	POLR2A	chr1:158979459-158980230	Hela-S3	cervix:	n/a	n/a
44	CHD2	chr1:158978435-158980163	GM12878	blood:	n/a	n/a
45	STAT1	chr1:158979114-158980276	Hela-S3	cervix:	n/a	chr1:158979608-158979619 chr1:158979355-158979364
46	STAT3	chr1:158979009-158980766	MCF10A-Er-Src	breast:	n/a	chr1:158979842-158979853 chr1:158979355-158979364
47	MYC	chr1:158979105-158980701	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr1:158979204-158980111	GM12878	blood:	n/a	n/a
49	GATA1	chr1:158979309-158980639	K562	blood:	n/a	n/a
50	CHD1	chr1:158978577-158980909	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158979699..158980284-chr16:31191231..31192125,2	Hela-S3	cervix:
2	chr1:158978448..158981430-chr1:159044743..159047016,2	K562	blood:

Variant related genes	Relation type
IFI16	TF binding region
ENSG00000089280	Chromatin interaction
ENSG00000163568	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158970800-158980800	Weak transcription	Pancreas	Pancrea
2	chr1:158976000-158983000	Weak transcription	Spleen	Spleen
3	chr1:158976000-159000800	Weak transcription	Gastric	stomach
4	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:158977800-158982400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:158978200-158980400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:158978200-158981400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr1:158978600-158980200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr1:158978600-158984200	Active TSS	Rectal Smooth Muscle	rectum
10	chr1:158978800-158983800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:158978800-158985800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr1:158979000-158980800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:158979000-158981200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr1:158979200-158980600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:158979200-158981000	Active TSS	Aorta	Aorta
16	chr1:158979200-158981200	Active TSS	Colonic Mucosa	Colon
17	chr1:158979200-158981200	Active TSS	Psoas Muscle	Psoas
18	chr1:158979200-158982600	Active TSS	Fetal Stomach	stomach
19	chr1:158979200-158982800	Active TSS	NHLF	lung
20	chr1:158979200-158983200	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr1:158979200-158983400	Active TSS	Right Atrium	heart
22	chr1:158979200-158984000	Active TSS	Stomach Smooth Muscle	stomach
23	chr1:158979400-158980200	Active TSS	A549	lung
24	chr1:158979400-158980600	Active TSS	Brain Substantia Nigra	brain
25	chr1:158979400-158980800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:158979400-158980800	Active TSS	Brain Cingulate Gyrus	brain
27	chr1:158979400-158981000	Active TSS	Brain Angular Gyrus	brain
28	chr1:158979400-158981000	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr1:158979400-158981000	Active TSS	Dnd41	blood
30	chr1:158979400-158981200	Active TSS	Fetal Intestine Small	intestine
31	chr1:158979400-158981200	Active TSS	Left Ventricle	heart
32	chr1:158979400-158981400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:158979400-158981600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:158979400-158981600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:158979400-158982000	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr1:158979400-158982200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:158979400-158982200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:158979400-158982200	Active TSS	NHDF-Ad	bronchial
39	chr1:158979400-158982400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:158979400-158982400	Active TSS	Fetal Kidney	kidney
41	chr1:158979400-158982400	Active TSS	Fetal Lung	lung
42	chr1:158979400-158982400	Active TSS	HSMM	muscle
43	chr1:158979400-158982400	Active TSS	HSMMtube	muscle
44	chr1:158979400-158982800	Active TSS	Fetal Intestine Large	intestine
45	chr1:158979400-158983000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:158979400-158983000	Active TSS	Primary T cells fromperipheralblood	blood
47	chr1:158979400-158983000	Active TSS	Ovary	ovary
48	chr1:158979400-158983000	Active TSS	Thymus	Thymus
49	chr1:158979400-158983200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:158979400-158983200	Active TSS	Skeletal Muscle Male	skeletal muscle

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