Variant report

Variant	rs540004793
Chromosome Location	chr1:172420085-172420086
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	GATA3	chr1:172419512-172420777	MCF-7	breast:	n/a	chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
2	SMC3	chr1:172419983-172420501	HepG2	liver:	n/a	n/a
3	MAZ	chr1:172419919-172420582	K562	blood:	n/a	chr1:172420446-172420455
4	MAZ	chr1:172419983-172420712	IMR90	lung:	n/a	chr1:172420446-172420455 chr1:172420649-172420658
5	KAP1	chr1:172418771-172420713	HEK293	kidney:	n/a	chr1:172420445-172420454
6	CREB1	chr1:172418049-172420111	HepG2	liver:	n/a	n/a
7	NR2F2	chr1:172418858-172420695	K562	blood:	n/a	n/a
8	POLR2A	chr1:172418279-172420393	HepG2	liver:	n/a	n/a
9	ARID3A	chr1:172420022-172420602	K562	blood:	n/a	n/a
10	ZEB1	chr1:172417854-172420270	HepG2	liver:	n/a	chr1:172418210-172418221 chr1:172418038-172418049 chr1:172418471-172418479 chr1:172419031-172419038
11	CTCF	chr1:172420040-172420190	GM12872	blood:	n/a	n/a
12	EP300	chr1:172420068-172420688	A549	lung:	n/a	chr1:172420565-172420575
13	POLR2A	chr1:172418315-172420143	HL-60	blood:	n/a	n/a
14	SP1	chr1:172420024-172420693	A549	lung:	n/a	n/a
15	GATA3	chr1:172419643-172420603	MCF-7	breast:	n/a	chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
16	MAX	chr1:172418247-172420387	HepG2	liver:	n/a	n/a
17	GATA3	chr1:172420002-172420856	A549	lung:	n/a	chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
18	POLR2A	chr1:172418157-172420104	HepG2	liver:	n/a	n/a
19	JUND	chr1:172420084-172420745	MCF-7	breast:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172420224-172420234 chr1:172420614-172420626 chr1:172420445-172420456 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
20	MAZ	chr1:172418831-172420595	HepG2	liver:	n/a	chr1:172420446-172420455
21	TEAD4	chr1:172419182-172420120	HepG2	liver:	n/a	n/a
22	NR2F2	chr1:172419483-172420685	MCF-7	breast:	n/a	n/a
23	CBX3	chr1:172419982-172420608	K562	blood:	n/a	n/a
24	CTCF	chr1:172417456-172420817	A549	lung:	n/a	chr1:172419229-172419247 chr1:172420251-172420259 chr1:172419777-172419790 chr1:172419234-172419242 chr1:172419231-172419252
25	ZNF217	chr1:172419800-172420593	MCF-7	breast:	n/a	n/a
26	FOSL2	chr1:172420061-172420685	MCF-7	breast:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172420224-172420234 chr1:172420614-172420626 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
27	FOSL2	chr1:172420040-172420683	MCF-7	breast:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172420224-172420234 chr1:172420614-172420626 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
28	RCOR1	chr1:172419030-172420642	K562	blood:	n/a	n/a
29	MAX	chr1:172418995-172420243	A549	lung:	n/a	n/a
30	MAX	chr1:172418976-172420383	MCF-7	breast:	n/a	n/a
31	ZNF143	chr1:172419919-172420349	K562	blood:	n/a	n/a
32	TCF7L2	chr1:172419268-172421000	HEK293	kidney:	n/a	chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172420413-172420429
33	TCF7L2	chr1:172419951-172420846	HepG2	liver:	n/a	chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172420413-172420429
34	GATA3	chr1:172417920-172420674	MCF-7	breast:	n/a	chr1:172418403-172418412 chr1:172420461-172420468 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172418190-172418211 chr1:172420461-172420471 chr1:172420223-172420232
35	EP300	chr1:172420051-172420538	K562	blood:	n/a	n/a
36	RAD21	chr1:172418861-172420176	MCF-7	breast:	n/a	chr1:172419230-172419249 chr1:172419232-172419239 chr1:172419781-172419791
37	GATA1	chr1:172419113-172420914	PBDE	blood:	n/a	chr1:172420461-172420468 chr1:172420893-172420904 chr1:172420461-172420468 chr1:172420459-172420469 chr1:172420461-172420468 chr1:172420461-172420471 chr1:172420223-172420232
38	MYC	chr1:172419939-172420302	K562	blood:	n/a	n/a
39	TCF7L2	chr1:172417976-172420696	Hela-S3	cervix:	n/a	chr1:172418405-172418414 chr1:172418727-172418736 chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172418724-172418740 chr1:172418725-172418739 chr1:172420413-172420429
40	MAX	chr1:172418231-172420178	HepG2	liver:	n/a	n/a
41	FOSL2	chr1:172419794-172420698	A549	lung:	n/a	chr1:172420224-172420234 chr1:172420447-172420455 chr1:172419909-172419921 chr1:172420224-172420234 chr1:172420614-172420626 chr1:172420224-172420234 chr1:172420445-172420457 chr1:172420224-172420234
42	TCF12	chr1:172417909-172420747	A549	lung:	n/a	chr1:172419611-172419618 chr1:172419480-172419490
43	POLR2A	chr1:172418384-172420817	PBDE	blood:	n/a	n/a
44	POLR2A	chr1:172418071-172420575	HepG2	liver:	n/a	n/a
45	MAFF	chr1:172419868-172420094	HepG2	liver:	n/a	n/a
46	RFX5	chr1:172420031-172420222	K562	blood:	n/a	n/a
47	RCOR1	chr1:172418259-172420675	IMR90	lung:	n/a	n/a
48	TCF7L2	chr1:172420083-172420712	MCF-7	breast:	n/a	chr1:172420414-172420428 chr1:172420417-172420426 chr1:172420413-172420429 chr1:172420416-172420425 chr1:172420413-172420429
49	FOXA2	chr1:172419970-172420957	HepG2	liver:	n/a	chr1:172420470-172420482
50	EP300	chr1:172420080-172420648	A549	lung:	n/a	chr1:172420565-172420575

No.	Distal block	Cell Line	Cell type
1	chr1:172419256..172421468-chr1:172500783..172504604,4	K562	blood:
2	chr1:172416845..172420491-chr1:172421660..172424212,3	MCF-7	breast:
3	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
4	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:

Variant related genes	Relation type
C1orf105	TF binding region
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 1 )
Associated
traits (count: 0)

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947449	chr1:172419586-172424910	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172413600-172421800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:172413600-172421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:172415400-172420400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:172416400-172420600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:172416400-172420600	Enhancers	HMEC	breast
6	chr1:172417200-172420600	Enhancers	NHEK	skin
7	chr1:172417200-172421800	Weak transcription	Psoas Muscle	Psoas
8	chr1:172417200-172423200	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr1:172417600-172420800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:172417800-172420600	Enhancers	Placenta	Placenta
11	chr1:172417800-172420600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:172417800-172420800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:172417800-172420800	Enhancers	Fetal Kidney	kidney
14	chr1:172418000-172420200	Flanking Active TSS	A549	lung
15	chr1:172418000-172420400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:172418000-172420400	Enhancers	Stomach Mucosa	stomach
17	chr1:172418000-172420800	Enhancers	HUVEC	blood vessel
18	chr1:172418000-172422200	Enhancers	NH-A	brain
19	chr1:172418400-172420400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:172418400-172420600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:172418600-172420200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:172418600-172420400	Enhancers	Esophagus	oesophagus
23	chr1:172418800-172420200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:172418800-172420400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:172418800-172420400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:172418800-172420400	Enhancers	Left Ventricle	heart
27	chr1:172418800-172420600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr1:172419000-172420400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr1:172419000-172420400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr1:172419000-172420400	Enhancers	Pancreas	Pancrea
31	chr1:172419000-172420600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:172419000-172420600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:172419000-172420600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr1:172419000-172420600	Enhancers	Liver	Liver
35	chr1:172419000-172420600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:172419000-172420600	Enhancers	NHLF	lung
37	chr1:172419200-172420200	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:172419200-172420400	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr1:172419200-172420400	Enhancers	Dnd41	blood
40	chr1:172419200-172420600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:172419200-172420800	Enhancers	Fetal Heart	heart
42	chr1:172419200-172420800	Enhancers	Osteobl	bone
43	chr1:172419400-172420200	Enhancers	Right Atrium	heart
44	chr1:172419400-172420400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:172419400-172420400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:172419400-172420600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr1:172419400-172420600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:172419400-172422200	Weak transcription	Brain Substantia Nigra	brain
49	chr1:172419600-172420200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:172419600-172420400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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