Variant report

Variant	rs78554911
Chromosome Location	chr19:38875871-38875872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38875223-38876154	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:38875329-38876047	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:38875834-38875916	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:38875003-38876118	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:38874377-38876119	K562	blood:	n/a	n/a
6	POLR2A	chr19:38874843-38876344	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr19:38874550-38877193	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr19:38874404-38876202	A549	lung:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
9	POLR2A	chr19:38874762-38876307	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:38874034-38876600	K562	blood:	n/a	n/a
11	POLR2A	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr19:38875778-38875903	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr19:38874152-38877033	GM12891	blood:	n/a	n/a
14	POLR2A	chr19:38874035-38876338	K562	blood:	n/a	n/a
15	POLR2A	chr19:38874785-38879102	A549	lung:	n/a	n/a
16	POLR2A	chr19:38874581-38876014	PBDE	blood:	n/a	n/a
17	POLR2A	chr19:38874623-38876880	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:38875283-38875886	A549	lung:	n/a	n/a
19	POLR2A	chr19:38874823-38876241	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:38875415-38876117	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:38869603-38879135	K562	blood:	n/a	n/a
22	POLR2A	chr19:38874605-38876529	K562	blood:	n/a	n/a
23	POLR2A	chr19:38874960-38876021	K562	blood:	n/a	n/a
24	SIX5	chr19:38874569-38875896	A549	lung:	n/a	chr19:38875719-38875735
25	POLR2A	chr19:38875823-38876160	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr19:38873616-38876905	A549	lung:	n/a	n/a
27	POLR2A	chr19:38874045-38876287	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:38874282-38876073	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:38874705-38876483	HL-60	blood:	n/a	n/a
30	ZNF263	chr19:38874793-38875899	HEK293-T-REx	kidney:	n/a	n/a
31	RAD21	chr19:38874893-38875880	A549	lung:	n/a	chr19:38875536-38875546 chr19:38875532-38875551 chr19:38875534-38875546
32	POLR2A	chr19:38874471-38877088	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr19:38874819-38875991	H1-hESC	embryonic stem cell:	n/a	n/a
34	CHD2	chr19:38875159-38876157	K562	blood:	n/a	n/a
35	POLR2A	chr19:38873453-38879163	K562	blood:	n/a	n/a
36	POLR2A	chr19:38874175-38877146	GM12892	blood:	n/a	n/a
37	POLR2A	chr19:38873627-38879112	K562	blood:	n/a	n/a
38	POLR2A	chr19:38873798-38877126	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr19:38874901-38876812	GM19193	blood:	n/a	n/a
40	POLR2A	chr19:38874768-38876500	U87	brain:	n/a	n/a
41	NR2F2	chr19:38875384-38876003	K562	blood:	n/a	n/a
42	POLR2A	chr19:38874782-38876008	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:38874808-38875997	GM18505	blood:	n/a	n/a
44	BCL3	chr19:38874813-38876285	A549	lung:	n/a	n/a
45	POLR2A	chr19:38874068-38876982	GM12892	blood:	n/a	n/a
46	POLR2A	chr19:38874772-38877051	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:38874370-38877112	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:38873479-38877165	GM12878	blood:	n/a	n/a
49	BCL3	chr19:38875067-38876014	A549	lung:	n/a	n/a
50	POLR2A	chr19:38873532-38876808	GM12892	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
2	chr19:36630602..36632414-chr19:38875371..38878496,3	MCF-7	breast:
3	chr19:38719348..38721458-chr19:38874867..38876458,2	K562	blood:
4	chr19:38724179..38724967-chr19:38875093..38875913,3	K562	blood:
5	chr19:38804471..38807313-chr19:38874109..38876554,2	MCF-7	breast:
6	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:
7	chr19:38854277..38857061-chr19:38874070..38875932,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267090	TF binding region
SPRED3	TF binding region
ENSG00000126247	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000167645	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	esv3361438	chr19:38875337-38877885	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38866400-38876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:38867000-38877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:38867000-38878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:38867200-38877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:38867200-38877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:38867200-38877400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:38867600-38876000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr19:38867600-38876200	Strong transcription	Brain Cingulate Gyrus	brain
9	chr19:38867600-38877400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:38867800-38876200	Strong transcription	Adipose Nuclei	Adipose
11	chr19:38867800-38876200	Strong transcription	Brain Hippocampus Middle	brain
12	chr19:38867800-38876600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:38867800-38877000	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr19:38868000-38876000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:38868000-38876000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr19:38868000-38876200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:38868000-38877600	Weak transcription	Right Atrium	heart
18	chr19:38868400-38876400	Strong transcription	Colonic Mucosa	Colon
19	chr19:38868800-38876000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr19:38869400-38876000	Strong transcription	K562	blood
21	chr19:38869400-38876400	Strong transcription	HMEC	breast
22	chr19:38869600-38876200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:38869600-38876400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:38869600-38876600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:38869600-38877400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:38869600-38877800	Strong transcription	NHLF	lung
27	chr19:38869800-38876000	Strong transcription	GM12878-XiMat	blood
28	chr19:38869800-38876200	Strong transcription	Brain Substantia Nigra	brain
29	chr19:38869800-38876200	Strong transcription	Pancreas	Pancrea
30	chr19:38870000-38876000	Strong transcription	Gastric	stomach
31	chr19:38870200-38876200	Strong transcription	Right Ventricle	heart
32	chr19:38870200-38877400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:38870400-38876800	Strong transcription	Ovary	ovary
34	chr19:38871600-38876000	ZNF genes & repeats	Spleen	Spleen
35	chr19:38873000-38876400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:38873000-38876400	Genic enhancers	Placenta	Placenta
37	chr19:38873000-38877800	Weak transcription	Hela-S3	cervix
38	chr19:38873200-38877600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:38873600-38876200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
40	chr19:38873800-38876000	ZNF genes & repeats	Fetal Stomach	stomach
41	chr19:38874000-38876200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:38874000-38876600	Strong transcription	Esophagus	oesophagus
43	chr19:38874000-38877600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr19:38874200-38876000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:38874200-38876200	Strong transcription	NHEK	skin
46	chr19:38874200-38876400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:38874200-38876400	Strong transcription	Lung	lung
48	chr19:38874400-38876200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:38874400-38876400	Weak transcription	Primary B cells from cord blood	blood
50	chr19:38874400-38877600	Weak transcription	HUVEC	blood vessel

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