Variant report

Variant	rs529475163
Chromosome Location	chr19:38885354-38885355
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	RAD21	chr19:38885241-38885571	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr19:38885171-38885400	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
4	USF1	chr19:38885082-38885503	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr19:38885175-38885442	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZNF143	chr19:38885071-38885557	H1-hESC	embryonic stem cell:	n/a	n/a
7	USF2	chr19:38885202-38885362	HepG2	liver:	n/a	n/a
8	NANOG	chr19:38885181-38885548	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:38885207-38885504	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr19:38885113-38885384	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr19:38885192-38885399	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:38885180-38885403	HUVEC	blood vessel:	n/a	n/a
13	MAX	chr19:38885041-38885621	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:38885152-38885590	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF263	chr19:38884380-38885405	HEK293-T-REx	kidney:	n/a	n/a
16	MAX	chr19:38885138-38885482	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:38884992-38885648	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr19:38885159-38885679	H1-hESC	embryonic stem cell:	n/a	n/a
19	SP1	chr19:38885014-38885614	H1-hESC	embryonic stem cell:	n/a	chr19:38885481-38885495 chr19:38885243-38885253 chr19:38885243-38885253 chr19:38885298-38885309
20	SP4	chr19:38885026-38885522	H1-hESC	embryonic stem cell:	n/a	chr19:38885298-38885309
21	MAX	chr19:38885026-38885545	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr19:38885129-38885396	K562	blood:	n/a	n/a
23	JUND	chr19:38885043-38885449	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr19:38885314-38885722	H1-hESC	embryonic stem cell:	n/a	n/a
25	USF1	chr19:38885016-38885554	H1-hESC	embryonic stem cell:	n/a	n/a
26	MXI1	chr19:38885156-38885470	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:38885042-38885865	H1-hESC	embryonic stem cell:	n/a	n/a
28	EGR1	chr19:38884969-38885524	H1-hESC	embryonic stem cell:	n/a	chr19:38885240-38885250 chr19:38885238-38885251 chr19:38885239-38885250 chr19:38885241-38885250 chr19:38885238-38885251 chr19:38885237-38885252 chr19:38885238-38885252 chr19:38885238-38885251 chr19:38885234-38885256 chr19:38885238-38885251 chr19:38885240-38885250
29	SIN3A	chr19:38885106-38885577	H1-hESC	embryonic stem cell:	n/a	n/a
30	EGR1	chr19:38885077-38885383	K562	blood:	n/a	chr19:38885240-38885250 chr19:38885238-38885251 chr19:38885239-38885250 chr19:38885241-38885250 chr19:38885238-38885251 chr19:38885237-38885252 chr19:38885238-38885252 chr19:38885238-38885251 chr19:38885234-38885256 chr19:38885238-38885251 chr19:38885240-38885250
31	USF2	chr19:38885094-38885481	H1-hESC	embryonic stem cell:	n/a	n/a
32	SP4	chr19:38885211-38885610	H1-hESC	embryonic stem cell:	n/a	chr19:38885298-38885309
33	CHD2	chr19:38885330-38885616	H1-hESC	embryonic stem cell:	n/a	n/a
34	E2F6	chr19:38885021-38885618	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYC	chr19:38885183-38885381	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr19:38883299-38886167	PFSK-1	brain:	n/a	n/a
37	YY1	chr19:38885135-38885650	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38864094..38865598-chr19:38884345..38886575,2	K562	blood:
2	chr19:38881527..38884112-chr19:38884478..38886116,2	K562	blood:
3	chr19:38724585..38727174-chr19:38883492..38886224,2	K562	blood:
4	chr19:38877412..38880246-chr19:38884643..38887201,2	K562	blood:

Variant related genes	Relation type
ENSG00000267473	TF binding region
ENSG00000099341	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000179168	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	esv3425239	chr19:38885137-38887985	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38880000-38886400	Weak transcription	Gastric	stomach
2	chr19:38880200-38885400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr19:38880200-38887600	Weak transcription	Right Atrium	heart
4	chr19:38880800-38889200	Weak transcription	Brain Angular Gyrus	brain
5	chr19:38881000-38887000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:38881000-38887600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:38881000-38893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38881000-38893200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:38881000-38893200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:38881000-38893200	Weak transcription	HSMMtube	muscle
11	chr19:38881200-38887200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:38881600-38886200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:38882600-38888000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:38882800-38887400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:38883000-38885400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:38883000-38885400	Enhancers	Fetal Intestine Small	intestine
17	chr19:38883000-38888000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:38883200-38885400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:38883200-38887800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:38883600-38885400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr19:38883600-38885600	Enhancers	Duodenum Mucosa	Duodenum
22	chr19:38883600-38891600	Weak transcription	HUVEC	blood vessel
23	chr19:38883600-38893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:38883800-38885400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:38883800-38886800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:38883800-38887200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:38883800-38887600	Strong transcription	NHLF	lung
28	chr19:38883800-38887800	Strong transcription	Osteobl	bone
29	chr19:38883800-38888400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:38884000-38885400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:38884000-38885800	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr19:38884000-38886400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38884000-38891600	Weak transcription	A549	lung
34	chr19:38884600-38885400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:38884600-38885400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:38884600-38885400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr19:38884600-38886200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:38884600-38887200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:38884800-38885400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr19:38884800-38885400	Bivalent Enhancer	Placenta	Placenta
41	chr19:38884800-38886200	Enhancers	Esophagus	oesophagus
42	chr19:38884800-38886200	Bivalent Enhancer	Stomach Mucosa	stomach
43	chr19:38884800-38886600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:38884800-38893200	Weak transcription	NH-A	brain
45	chr19:38885000-38885400	Enhancers	H9 Cell Line	embryonic stem cell
46	chr19:38885000-38885400	Enhancers	Primary T cells fromperipheralblood	blood
47	chr19:38885000-38885400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr19:38885000-38885400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:38885000-38885400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:38885000-38885400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin

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