Variant report

Variant	rs542991772
Chromosome Location	chr19:42754911-42754912
allele	G/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	TCF12	chr19:42754155-42755527	A549	lung:	n/a	chr19:42754917-42754927
2	POLR2A	chr19:42754694-42755612	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:42754585-42755487	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:42749868-42759399	HepG2	liver:	n/a	n/a
5	PBX3	chr19:42754718-42755359	SK-N-SH	brain:	n/a	chr19:42755015-42755035
6	POLR2A	chr19:42754561-42755172	A549	lung:	n/a	n/a
7	MAZ	chr19:42754805-42760905	IMR90	lung:	n/a	chr19:42759369-42759378 chr19:42755056-42755065 chr19:42756308-42756319 chr19:42758228-42758238 chr19:42759385-42759395 chr19:42758595-42758605 chr19:42757003-42757010 chr19:42757000-42757013 chr19:42757002-42757011 chr19:42760033-42760042 chr19:42757284-42757293 chr19:42757002-42757012 chr19:42759330-42759339 chr19:42759102-42759117 chr19:42758566-42758576 chr19:42758254-42758264 chr19:42757001-42757012 chr19:42759119-42759129 chr19:42759365-42759374
8	EP300	chr19:42754659-42755321	SK-N-SH	brain:	n/a	n/a
9	MXI1	chr19:42754690-42755757	IMR90	lung:	n/a	n/a
10	USF1	chr19:42754907-42755172	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr19:42754652-42755299	U87	brain:	n/a	n/a
12	EP300	chr19:42754805-42755134	SK-N-SH_RA	brain:	n/a	n/a
13	REST	chr19:42754697-42755205	A549	lung:	n/a	chr19:42754933-42754946 chr19:42755131-42755141
14	MAX	chr19:42754752-42755278	SK-N-SH	brain:	n/a	chr19:42755056-42755065
15	POLR2A	chr19:42754730-42755279	U87	brain:	n/a	n/a
16	NFIC	chr19:42754748-42755302	SK-N-SH	brain:	n/a	n/a
17	MAX	chr19:42754767-42755296	SK-N-SH	brain:	n/a	chr19:42755056-42755065
18	POLR2A	chr19:42752554-42755496	A549	lung:	n/a	n/a
19	USF1	chr19:42754846-42755122	SK-N-SH_RA	brain:	n/a	n/a
20	POLR2A	chr19:42754371-42755215	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr19:42746451-42758038	PFSK-1	brain:	n/a	n/a
22	MAX	chr19:42754668-42755561	A549	lung:	n/a	chr19:42755056-42755065
23	EP300	chr19:42754263-42755191	A549	lung:	n/a	n/a
24	FOXP2	chr19:42754779-42755180	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr19:42754500-42754933	GM12892	blood:	n/a	n/a
26	POLR2A	chr19:42754691-42755235	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr19:42754294-42755132	A549	lung:	n/a	n/a
28	BCL3	chr19:42754594-42755393	A549	lung:	n/a	n/a
29	MTA3	chr19:42754731-42755203	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:42754031-42755186	A549	lung:	n/a	n/a
31	POLR2A	chr19:42754133-42755267	HUVEC	blood vessel:	n/a	n/a
32	JUND	chr19:42754462-42755604	A549	lung:	n/a	n/a
33	NFIC	chr19:42754764-42755534	SK-N-SH	brain:	n/a	n/a
34	BCL3	chr19:42753721-42755351	A549	lung:	n/a	n/a
35	POLR2A	chr19:42754827-42755119	A549	lung:	n/a	n/a
36	POLR2A	chr19:42753422-42755373	HepG2	liver:	n/a	n/a
37	POLR2A	chr19:42746087-42755524	HepG2	liver:	n/a	n/a
38	POLR2A	chr19:42748210-42757941	K562	blood:	n/a	n/a
39	MYC	chr19:42754804-42755237	HUVEC	blood vessel:	n/a	chr19:42755056-42755065
40	SIX5	chr19:42753885-42755466	A549	lung:	n/a	n/a
41	POLR2A	chr19:42745727-42755683	PFSK-1	brain:	n/a	n/a
42	SIN3AK20	chr19:42754735-42755028	PFSK-1	brain:	n/a	n/a
43	MAX	chr19:42754682-42755432	A549	lung:	n/a	chr19:42755056-42755065
44	USF1	chr19:42754828-42755293	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr19:42754907-42755047	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr19:42753984-42755144	GM12891	blood:	n/a	n/a
47	POLR2A	chr19:42754436-42755444	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr19:42753795-42754994	GM12891	blood:	n/a	n/a
49	EBF1	chr19:42754860-42755161	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:42749752-42759489	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42754219..42757685-chr19:42805206..42807524,5	MCF-7	breast:
2	chr19:42747132..42763787-chr19:42768368..42776785,67	MCF-7	breast:
3	chr19:42722598..42724600-chr19:42754486..42756039,2	MCF-7	breast:
4	chr19:42754290..42756701-chr19:42804402..42806386,2	K562	blood:
5	chr19:42744297..42761073-chr19:42776978..42802286,113	MCF-7	breast:
6	chr19:42743599..42762610-chr19:42780302..42801550,102	MCF-7	breast:

Variant related genes	Relation type
ERF	TF binding region
ENSG00000188368	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000160570	Chromatin interaction
ENSG00000167625	Chromatin interaction
ENSG00000079462	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
9	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
11	nsv911784	chr19:42741124-42787664	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
12	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
13	nsv911786	chr19:42744234-42797959	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
14	esv1802977	chr19:42754437-42789945	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 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	chr19:42749000-42757000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:42749400-42755000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:42749400-42755800	Enhancers	Fetal Heart	heart
4	chr19:42749400-42756200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:42749600-42755000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:42750000-42755000	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr19:42750400-42755200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:42750600-42755600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:42750800-42755000	Strong transcription	Dnd41	blood
10	chr19:42751000-42756200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:42751200-42755400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:42751400-42755000	Weak transcription	GM12878-XiMat	blood
13	chr19:42752400-42755000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:42752600-42755000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:42752600-42755600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:42752600-42757400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:42753000-42755000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:42753400-42755000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:42753600-42755000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:42753600-42755200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:42753600-42756400	Genic enhancers	Spleen	Spleen
22	chr19:42753800-42755000	Genic enhancers	Gastric	stomach
23	chr19:42753800-42756000	Genic enhancers	HepG2	liver
24	chr19:42753800-42757000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr19:42753800-42757800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:42754000-42755000	Genic enhancers	Primary T cells from cord blood	blood
27	chr19:42754000-42755000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr19:42754000-42755000	Genic enhancers	Fetal Thymus	thymus
29	chr19:42754000-42755800	Genic enhancers	Fetal Intestine Small	intestine
30	chr19:42754000-42755800	Genic enhancers	Fetal Stomach	stomach
31	chr19:42754000-42756000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr19:42754000-42756600	Enhancers	Left Ventricle	heart
33	chr19:42754200-42755000	Enhancers	Fetal Brain Female	brain
34	chr19:42754200-42756200	Enhancers	Primary hematopoietic stem cells	blood
35	chr19:42754200-42756200	Enhancers	Fetal Brain Male	brain
36	chr19:42754200-42756800	Enhancers	Esophagus	oesophagus
37	chr19:42754200-42757200	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr19:42754200-42757400	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr19:42754200-42757800	Transcr. at gene 5' and 3'	A549	lung
40	chr19:42754400-42755000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
41	chr19:42754400-42755000	Genic enhancers	Colonic Mucosa	Colon
42	chr19:42754400-42755200	Weak transcription	Primary B cells from cord blood	blood
43	chr19:42754400-42755200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:42754400-42755200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:42754400-42755200	Enhancers	Psoas Muscle	Psoas
46	chr19:42754400-42755400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:42754400-42755400	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr19:42754400-42755400	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr19:42754400-42755600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:42754400-42755800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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