Variant report

Variant	rs199606056
Chromosome Location	chr19:38874993-38874994
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	RAD21	chr19:38874881-38875744	H1-hESC	embryonic stem cell:	n/a	chr19:38875536-38875546 chr19:38875532-38875551 chr19:38875534-38875546
2	POLR2A	chr19:38874982-38875180	A549	lung:	n/a	n/a
3	CTCF	chr19:38874960-38875110	GM12873	blood:	n/a	n/a
4	CTCF	chr19:38874986-38875199	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:38874940-38875728	H1-hESC	embryonic stem cell:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
6	POLR2A	chr19:38874377-38876119	K562	blood:	n/a	n/a
7	CTCF	chr19:38874943-38875270	K562	blood:	n/a	n/a
8	POLR2A	chr19:38874843-38876344	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr19:38874550-38877193	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr19:38874404-38876202	A549	lung:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
11	POLR2A	chr19:38874762-38876307	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:38874642-38875082	U87	brain:	n/a	n/a
13	POLR2A	chr19:38874034-38876600	K562	blood:	n/a	n/a
14	POLR2A	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr19:38874152-38877033	GM12891	blood:	n/a	n/a
16	CTCF	chr19:38874940-38875090	HCT-116	colon:	n/a	n/a
17	POLR2A	chr19:38874035-38876338	K562	blood:	n/a	n/a
18	POLR2A	chr19:38874785-38879102	A549	lung:	n/a	n/a
19	POLR2A	chr19:38874581-38876014	PBDE	blood:	n/a	n/a
20	POLR2A	chr19:38874623-38876880	GM12891	blood:	n/a	n/a
21	POLR2A	chr19:38874823-38876241	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:38869603-38879135	K562	blood:	n/a	n/a
23	POLR2A	chr19:38874605-38876529	K562	blood:	n/a	n/a
24	JUND	chr19:38874724-38875293	A549	lung:	n/a	chr19:38874850-38874861 chr19:38874828-38874837
25	POLR2A	chr19:38874960-38876021	K562	blood:	n/a	n/a
26	YY1	chr19:38874791-38875219	A549	lung:	n/a	chr19:38874828-38874837
27	SIX5	chr19:38874569-38875896	A549	lung:	n/a	chr19:38875719-38875735
28	ELF1	chr19:38874784-38875738	A549	lung:	n/a	n/a
29	POLR2A	chr19:38873616-38876905	A549	lung:	n/a	n/a
30	POLR2A	chr19:38874045-38876287	GM12891	blood:	n/a	n/a
31	CTCF	chr19:38874960-38875110	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr19:38874282-38876073	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr19:38874682-38875197	A549	lung:	n/a	n/a
34	POLR2A	chr19:38874950-38875176	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr19:38874980-38875130	GM12872	blood:	n/a	n/a
36	POLR2A	chr19:38874705-38876483	HL-60	blood:	n/a	n/a
37	CTCF	chr19:38874934-38875731	K562	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
38	ZNF263	chr19:38874793-38875899	HEK293-T-REx	kidney:	n/a	n/a
39	RAD21	chr19:38874893-38875880	A549	lung:	n/a	chr19:38875536-38875546 chr19:38875532-38875551 chr19:38875534-38875546
40	POLR2A	chr19:38874901-38875772	MCF-7	breast:	n/a	n/a
41	CTCF	chr19:38874960-38875110	GM12864	blood:	n/a	n/a
42	POLR2A	chr19:38874471-38877088	SK-N-MC	brain:	n/a	n/a
43	CTCF	chr19:38874960-38875110	AG09309	skin:	n/a	n/a
44	POLR2A	chr19:38874819-38875991	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr19:38873453-38879163	K562	blood:	n/a	n/a
46	POLR2A	chr19:38874175-38877146	GM12892	blood:	n/a	n/a
47	CTCF	chr19:38874942-38875742	K562	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
48	POLR2A	chr19:38873627-38879112	K562	blood:	n/a	n/a
49	POLR2A	chr19:38873798-38877126	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr19:38874901-38876812	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
2	chr19:38719348..38721458-chr19:38874867..38876458,2	K562	blood:
3	chr19:38738211..38740106-chr19:38872606..38875319,2	K562	blood:
4	chr19:38804471..38807313-chr19:38874109..38876554,2	MCF-7	breast:
5	chr19:38870927..38872589-chr19:38873604..38875519,2	MCF-7	breast:
6	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:
7	chr19:38854277..38857061-chr19:38874070..38875932,2	K562	blood:

Variant related genes	Relation type
SPRED3	TF binding region
ENSG00000267090	TF binding region
ENSG00000130244	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000011332	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:114 , 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	chr19:38867000-38875600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:38867000-38877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38867000-38878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:38867200-38875200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr19:38867200-38875400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:38867200-38877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:38867200-38877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:38867200-38877400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:38867400-38875000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:38867400-38875800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr19:38867600-38875200	Strong transcription	Liver	Liver
13	chr19:38867600-38875400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:38867600-38875600	Strong transcription	Fetal Intestine Small	intestine
15	chr19:38867600-38875800	Strong transcription	Primary T cells from cord blood	blood
16	chr19:38867600-38876000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr19:38867600-38876200	Strong transcription	Brain Cingulate Gyrus	brain
18	chr19:38867600-38877400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:38867800-38875000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
20	chr19:38867800-38875000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:38867800-38875200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:38867800-38875200	Strong transcription	Thymus	Thymus
23	chr19:38867800-38875400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr19:38867800-38875600	Strong transcription	Colon Smooth Muscle	Colon
25	chr19:38867800-38875800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:38867800-38875800	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr19:38867800-38876200	Strong transcription	Adipose Nuclei	Adipose
28	chr19:38867800-38876200	Strong transcription	Brain Hippocampus Middle	brain
29	chr19:38867800-38876600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:38867800-38877000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr19:38868000-38875600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr19:38868000-38875800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:38868000-38876000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:38868000-38876000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:38868000-38876200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:38868000-38877600	Weak transcription	Right Atrium	heart
37	chr19:38868400-38875000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:38868400-38876400	Strong transcription	Colonic Mucosa	Colon
39	chr19:38868800-38875400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:38868800-38876000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:38869400-38875000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:38869400-38875200	Strong transcription	Left Ventricle	heart
43	chr19:38869400-38875200	Strong transcription	A549	lung
44	chr19:38869400-38875400	Strong transcription	Osteobl	bone
45	chr19:38869400-38876000	Strong transcription	K562	blood
46	chr19:38869400-38876400	Strong transcription	HMEC	breast
47	chr19:38869600-38875000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:38869600-38875000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:38869600-38875200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:38869600-38875200	Strong transcription	Fetal Thymus	thymus

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