Variant report

Variant	rs545446463
Chromosome Location	chr19:41903470-41903471
allele	C/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	ARID3A	chr19:41903379-41903850	K562	blood:	n/a	n/a
2	YY1	chr19:41903095-41903943	NT2-D1	testis:	n/a	chr19:41903275-41903289 chr19:41903722-41903742
3	POLR2A	chr19:41902875-41903978	HL-60	blood:	n/a	n/a
4	TBP	chr19:41902911-41903907	GM12878	blood:	n/a	n/a
5	SP1	chr19:41903000-41903835	GM12878	blood:	n/a	chr19:41903386-41903397 chr19:41903376-41903388 chr19:41903387-41903401
6	MAX	chr19:41902954-41903857	Hela-S3	cervix:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
7	EP300	chr19:41902921-41903824	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:41903024-41903774	PANC-1	pancreas:	n/a	n/a
9	YY1	chr19:41902968-41904180	H1-hESC	embryonic stem cell:	n/a	chr19:41903275-41903289 chr19:41903722-41903742
10	POLR2A	chr19:41902978-41904050	ProgFib	skin:	n/a	n/a
11	TCF12	chr19:41902773-41903967	A549	lung:	n/a	n/a
12	SP1	chr19:41903101-41903881	H1-hESC	embryonic stem cell:	n/a	chr19:41903386-41903397 chr19:41903376-41903388 chr19:41903387-41903401
13	MXI1	chr19:41902802-41904031	GM12878	blood:	n/a	chr19:41903347-41903356
14	MYC	chr19:41902954-41903793	HepG2	liver:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
15	FOXA2	chr19:41902916-41903950	A549	lung:	n/a	n/a
16	POLR2A	chr19:41902982-41904104	K562	blood:	n/a	n/a
17	USF2	chr19:41903074-41903537	Hela-S3	cervix:	n/a	chr19:41903345-41903356
18	NFIC	chr19:41903126-41903860	HepG2	liver:	n/a	n/a
19	TBP	chr19:41902943-41903930	Hela-S3	cervix:	n/a	n/a
20	SIX5	chr19:41902909-41903953	A549	lung:	n/a	n/a
21	FOXP2	chr19:41903105-41903487	PFSK-1	brain:	n/a	n/a
22	MAX	chr19:41902792-41903973	ECC-1	luminal epithelium:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
23	GABPA	chr19:41902786-41903872	A549	lung:	n/a	chr19:41903306-41903320 chr19:41903309-41903320 chr19:41903309-41903318 chr19:41903309-41903323
24	ATF2	chr19:41903355-41903781	GM12878	blood:	n/a	n/a
25	SIN3AK20	chr19:41903047-41903506	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr19:41903007-41903949	GM19099	blood:	n/a	n/a
27	FOS	chr19:41903164-41903791	MCF10A-Er-Src	breast:	n/a	n/a
28	SIN3AK20	chr19:41902853-41903569	PFSK-1	brain:	n/a	n/a
29	USF1	chr19:41902969-41903644	H1-hESC	embryonic stem cell:	n/a	n/a
30	MYC	chr19:41902844-41903931	K562	blood:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
31	MYC	chr19:41902423-41905263	A549	lung:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
32	FOXA1	chr19:41903169-41903509	T-47D	breast:	n/a	n/a
33	MTA3	chr19:41902755-41904023	GM12878	blood:	n/a	n/a
34	RELA	chr19:41902976-41903921	GM10847	blood:	n/a	n/a
35	ELK1	chr19:41903076-41903724	Hela-S3	cervix:	n/a	n/a
36	YY1	chr19:41902971-41904147	GM12892	blood:	n/a	chr19:41903275-41903289 chr19:41903722-41903742
37	POLR2A	chr19:41902918-41904054	H1-neurons	neurons:	n/a	n/a
38	YY1	chr19:41903186-41903939	K562	blood:	n/a	chr19:41903275-41903289 chr19:41903722-41903742
39	POLR2A	chr19:41902989-41904024	PANC-1	pancreas:	n/a	n/a
40	RCOR1	chr19:41903127-41903798	GM12878	blood:	n/a	n/a
41	USF1	chr19:41902956-41903603	ECC-1	luminal epithelium:	n/a	n/a
42	GABPA	chr19:41902958-41903547	K562	blood:	n/a	chr19:41903306-41903320 chr19:41903309-41903320 chr19:41903309-41903318 chr19:41903309-41903323
43	SIN3AK20	chr19:41902777-41903900	K562	blood:	n/a	n/a
44	PML	chr19:41903278-41903561	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:41903035-41903948	K562	blood:	n/a	n/a
46	YY1	chr19:41903324-41904096	GM12892	blood:	n/a	chr19:41903722-41903742
47	POLR2A	chr19:41902950-41904010	MCF-7	breast:	n/a	n/a
48	RELA	chr19:41902889-41903885	GM18951	blood:	n/a	n/a
49	RCOR1	chr19:41903069-41903871	K562	blood:	n/a	n/a
50	SIN3AK20	chr19:41902838-41903868	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:41903455-41903505	ovcar-3	ovarian:	n/a
2	chr19:41903455-41903505	NHBE	bronchial:	n/a
3	chr19:41903455-41903505	PANC-1	pancreas:	n/a
4	chr19:41903455-41903505	H1-hESC	embryonic stem cell:	embryo
5	chr19:41903455-41903505	AG04449	skin:	fetal
6	chr19:41903455-41903505	HRE	kidney:	n/a
7	chr19:41903455-41903505	U87	brain:	n/a
8	chr19:41903455-41903505	Hepatocyte	liver:	n/a
9	chr19:41903455-41903505	AG04450	lung:	fetal
10	chr19:41903455-41903505	Caco-2	colon:	n/a
11	chr19:41903455-41903505	BJ	skin:	n/a
12	chr19:41903455-41903505	PrEC	prostate:	n/a
13	chr19:41903455-41903505	GM12878	blood:	n/a
14	chr19:41903455-41903505	HRCEpiC	kidney:	n/a
15	chr19:41903455-41903505	AG09309	skin:	n/a
16	chr19:41903455-41903505	HPAEpiC	pulmonary alveolar:	n/a
17	chr19:41903455-41903505	HNPCEpiC	eye:	n/a
18	chr19:41903455-41903505	Jurkat	blood:	n/a
19	chr19:41903455-41903505	ECC-1	luminal epithelium:	n/a
20	chr19:41903455-41903505	HEEpiC	esophagus:	n/a
21	chr19:41903455-41903505	NB4	blood:	n/a
22	chr19:41903455-41903505	T-47D	breast:	n/a
23	chr19:41903455-41903505	HepG2	liver:	n/a
24	chr19:41903455-41903505	BE2_C	brain:	n/a
25	chr19:41903455-41903505	HIPEpiC	eye:	n/a
26	chr19:41903455-41903505	AG09319	gingival:	n/a
27	chr19:41903455-41903505	AG10803	skin:	n/a
28	chr19:41903455-41903505	PFSK-1	brain:	n/a
29	chr19:41903455-41903505	HCPEpiC	choroid plexus:	n/a
30	chr19:41903455-41903505	HMEC	breast:	n/a
31	chr19:41903455-41903505	CMK	blood:	n/a
32	chr19:41903455-41903505	LNCaP	prostate:	n/a
33	chr19:41903455-41903505	SKMC	muscle:	n/a
34	chr19:41903455-41903505	A549	lung:	n/a
35	chr19:41903455-41903505	HCM	heart:	n/a
36	chr19:41903455-41903505	K562	blood:	n/a
37	chr19:41903455-41903505	NH-A	brain:	n/a
38	chr19:41903455-41903505	MCF-7	breast:	n/a
39	chr19:41903455-41903505	HCF	heart:	n/a
40	chr19:41903455-41903505	NHDF-neo	bronchial:	n/a
41	chr19:41903455-41903505	HUVEC	blood vessel:	n/a
42	chr19:41903455-41903505	HEK293	kidney:	embryo
43	chr19:41903455-41903505	Hela-S3	cervix:	n/a
44	chr19:41903455-41903505	GM12891	blood:	n/a
45	chr19:41903455-41903505	GM19239	blood:	n/a
46	chr19:41903455-41903505	MCF10A-Er-Src	breast:	n/a
47	chr19:41903455-41903505	GM06990	blood:	n/a
48	chr19:41903455-41903505	IMR90	lung:	fetal
49	chr19:41903455-41903505	HL-60	blood:	n/a
50	chr19:41903455-41903505	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41899828..41905293-chr19:41906916..41917787,16	MCF-7	breast:
2	chr19:41868160..41870059-chr19:41902135..41903854,4	K562	blood:
3	chr19:41856329..41860180-chr19:41901826..41904297,4	K562	blood:
4	chr19:41767651..41769904-chr19:41902855..41905283,2	K562	blood:
5	chr19:41903201..41905318-chr19:41918567..41921516,2	MCF-7	breast:
6	chr19:41902636..41905103-chr19:41930716..41934044,4	MCF-7	breast:
7	chr19:41855447..41861218-chr19:41901143..41905435,7	MCF-7	breast:
8	chr19:41856174..41858570-chr19:41902142..41904818,3	MCF-7	breast:
9	chr19:41868160..41871597-chr19:41899998..41904284,10	K562	blood:
10	chr19:41868161..41871707-chr19:41902716..41905358,4	MCF-7	breast:
11	chr19:41901938..41905441-chr19:41944047..41947443,5	K562	blood:
12	chr19:41901991..41905119-chr19:41933008..41936084,3	MCF-7	breast:
13	chr19:41855237..41861298-chr19:41901562..41905286,5	K562	blood:
14	chr19:41903342..41904945-chr19:41934241..41936024,2	MCF-7	breast:
15	chr19:41902654..41904815-chr19:41927221..41929015,2	K562	blood:

Variant related genes	Relation type
ENSG00000268987	TF binding region
EXOSC5	TF binding region
BCKDHA	TF binding region
ENSG00000268987	CpG island
BCKDHA	CpG island
EXOSC5	CpG island
ENSG00000248098	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000268475	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000177191	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	nsv828551	chr19:41903176-41903656	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 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	chr19:41901600-41904000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41901600-41904200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:41901800-41904400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:41902000-41904400	Active TSS	Hela-S3	cervix
5	chr19:41902000-41904600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:41902200-41904400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr19:41902200-41904400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:41902200-41904400	Active TSS	HSMM	muscle
9	chr19:41902200-41904600	Active TSS	Pancreas	Pancrea
10	chr19:41902200-41904600	Active TSS	GM12878-XiMat	blood
11	chr19:41902200-41904600	Active TSS	K562	blood
12	chr19:41902200-41905200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:41902400-41903800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:41902400-41904200	Active TSS	Placenta Amnion	Placenta Amnion
15	chr19:41902400-41904400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:41902400-41904400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:41902400-41904400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:41902400-41904400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:41902400-41904400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:41902400-41904400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:41902400-41904400	Active TSS	Brain Cingulate Gyrus	brain
22	chr19:41902400-41904400	Active TSS	Brain Germinal Matrix	brain
23	chr19:41902400-41904400	Active TSS	Colonic Mucosa	Colon
24	chr19:41902400-41904400	Active TSS	Fetal Intestine Small	intestine
25	chr19:41902400-41904400	Active TSS	Fetal Kidney	kidney
26	chr19:41902400-41904400	Active TSS	Right Ventricle	heart
27	chr19:41902400-41904600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:41902400-41904600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr19:41902400-41904600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:41902400-41904600	Active TSS	Fetal Intestine Large	intestine
31	chr19:41902400-41904600	Active TSS	Psoas Muscle	Psoas
32	chr19:41902400-41904800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr19:41902400-41905000	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr19:41902400-41905000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr19:41902400-41905000	Active TSS	Ovary	ovary
36	chr19:41902400-41905200	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr19:41902600-41904000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:41902600-41904200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:41902600-41904200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:41902600-41904200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr19:41902600-41904200	Active TSS	Fetal Brain Male	brain
42	chr19:41902600-41904200	Active TSS	Thymus	Thymus
43	chr19:41902600-41904400	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr19:41902600-41904400	Active TSS	Brain Hippocampus Middle	brain
45	chr19:41902600-41904400	Active TSS	Esophagus	oesophagus
46	chr19:41902600-41904400	Active TSS	Fetal Brain Female	brain
47	chr19:41902600-41904400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr19:41902600-41904400	Active TSS	Right Atrium	heart
49	chr19:41902600-41904400	Active TSS	HSMMtube	muscle
50	chr19:41902600-41904600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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