Variant report

Variant	rs565356246
Chromosome Location	chr19:38875541-38875542
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	CTCF	chr19:38875460-38875610	HCPEpiC	choroid plexus:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
2	RAD21	chr19:38874881-38875744	H1-hESC	embryonic stem cell:	n/a	chr19:38875536-38875546 chr19:38875532-38875551 chr19:38875534-38875546
3	POLR2A	chr19:38875223-38876154	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:38875329-38876047	GM12891	blood:	n/a	n/a
5	CTCF	chr19:38875460-38875610	HUVEC	blood vessel:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
6	CTCF	chr19:38875460-38875610	AG09319	gingival:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
7	CTCF	chr19:38875480-38875630	GM12869	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
8	CTCF	chr19:38875464-38875618	GM10266	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
9	POLR2A	chr19:38875003-38876118	HepG2	liver:	n/a	n/a
10	CTCF	chr19:38875500-38875650	RPTEC	kidney:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
11	CTCF	chr19:38875460-38875610	NHLF	lung:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
12	CTCF	chr19:38875440-38875590	HPF	lung:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
13	CTCF	chr19:38875370-38875720	HepG2	liver:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
14	CTCF	chr19:38875423-38875663	NHEK	skin:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
15	CTCF	chr19:38875480-38875630	HEK293	kidney:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
16	MAZ	chr19:38875383-38875633	K562	blood:	n/a	n/a
17	CTCF	chr19:38874940-38875728	H1-hESC	embryonic stem cell:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
18	CTCF	chr19:38875380-38875669	HepG2	liver:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
19	POLR2A	chr19:38874377-38876119	K562	blood:	n/a	n/a
20	CTCF	chr19:38875474-38875612	ProgFib	skin:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
21	CHD1	chr19:38875344-38875553	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr19:38875440-38875590	HRE	kidney:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
23	RAD21	chr19:38875333-38875607	H1-hESC	embryonic stem cell:	n/a	chr19:38875536-38875546 chr19:38875532-38875551 chr19:38875534-38875546
24	RCOR1	chr19:38875389-38875718	HepG2	liver:	n/a	n/a
25	RAD21	chr19:38875008-38875720	H1-hESC	embryonic stem cell:	n/a	chr19:38875536-38875546 chr19:38875532-38875551 chr19:38875534-38875546
26	POLR2A	chr19:38874843-38876344	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr19:38875490-38875621	GM12878	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
28	CTCF	chr19:38875400-38875550	GM06990	blood:	n/a	chr19:38875529-38875550 chr19:38875536-38875549
29	CTCF	chr19:38875464-38875606	Hela-S3	cervix:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
30	CTCF	chr19:38875423-38875644	A549	lung:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
31	POLR2A	chr19:38874550-38877193	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr19:38874404-38876202	A549	lung:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
33	CTCF	chr19:38875420-38875570	GM12873	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
34	CTCF	chr19:38875460-38875610	HA-sp	spinal cord:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
35	CTCF	chr19:38875420-38875570	HUVEC	blood vessel:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
36	CTCF	chr19:38875480-38875630	HRPEpiC	eye:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
37	POLR2A	chr19:38874762-38876307	GM12878	blood:	n/a	n/a
38	CTCF	chr19:38875460-38875610	WI-38	lung:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
39	POLR2A	chr19:38874034-38876600	K562	blood:	n/a	n/a
40	CTCF	chr19:38875440-38875590	GM12868	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
41	CTCF	chr19:38875460-38875610	BE2_C	brain:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
42	CTCF	chr19:38875477-38875599	LNCaP	prostate:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
43	POLR2A	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
44	CTCF	chr19:38875420-38875570	GM12870	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
45	CTCF	chr19:38875440-38875590	GM12871	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
46	CTCF	chr19:38875407-38875707	K562	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
47	CTCF	chr19:38875520-38875670	GM12873	blood:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
48	ZNF143	chr19:38875406-38875671	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr19:38874152-38877033	GM12891	blood:	n/a	n/a
50	RAD21	chr19:38875324-38875704	HepG2	liver:	n/a	chr19:38875536-38875546 chr19:38875532-38875551 chr19:38875534-38875546

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	chr19:38724375..38725000-chr19:38875077..38875830,2	MCF-7	breast:
7	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:
8	chr19:38854277..38857061-chr19:38874070..38875932,2	K562	blood:

Variant related genes	Relation type
ENSG00000267090	TF binding region
SPRED3	TF binding region
ENSG00000126247	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000130244	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:104 , 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	chr19:38867200-38877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:38867200-38877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:38867200-38877400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:38867400-38875800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr19:38867600-38875600	Strong transcription	Fetal Intestine Small	intestine
10	chr19:38867600-38875800	Strong transcription	Primary T cells from cord blood	blood
11	chr19:38867600-38876000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr19:38867600-38876200	Strong transcription	Brain Cingulate Gyrus	brain
13	chr19:38867600-38877400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:38867800-38875600	Strong transcription	Colon Smooth Muscle	Colon
15	chr19:38867800-38875800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:38867800-38875800	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr19:38867800-38876200	Strong transcription	Adipose Nuclei	Adipose
18	chr19:38867800-38876200	Strong transcription	Brain Hippocampus Middle	brain
19	chr19:38867800-38876600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:38867800-38877000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr19:38868000-38875600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr19:38868000-38875800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:38868000-38876000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:38868000-38876000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:38868000-38876200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:38868000-38877600	Weak transcription	Right Atrium	heart
27	chr19:38868400-38876400	Strong transcription	Colonic Mucosa	Colon
28	chr19:38868800-38876000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr19:38869400-38876000	Strong transcription	K562	blood
30	chr19:38869400-38876400	Strong transcription	HMEC	breast
31	chr19:38869600-38875600	Strong transcription	Psoas Muscle	Psoas
32	chr19:38869600-38875800	Strong transcription	Brain Angular Gyrus	brain
33	chr19:38869600-38876200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:38869600-38876400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:38869600-38876600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:38869600-38877400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:38869600-38877800	Strong transcription	NHLF	lung
38	chr19:38869800-38875800	Strong transcription	Brain Anterior Caudate	brain
39	chr19:38869800-38876000	Strong transcription	GM12878-XiMat	blood
40	chr19:38869800-38876200	Strong transcription	Brain Substantia Nigra	brain
41	chr19:38869800-38876200	Strong transcription	Pancreas	Pancrea
42	chr19:38870000-38876000	Strong transcription	Gastric	stomach
43	chr19:38870200-38876200	Strong transcription	Right Ventricle	heart
44	chr19:38870200-38877400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:38870400-38875800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:38870400-38876800	Strong transcription	Ovary	ovary
47	chr19:38871600-38876000	ZNF genes & repeats	Spleen	Spleen
48	chr19:38873000-38876400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:38873000-38876400	Genic enhancers	Placenta	Placenta
50	chr19:38873000-38877800	Weak transcription	Hela-S3	cervix

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