Variant report

Variant	rs561147041
Chromosome Location	chr19:45681662-45681663
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	CTCF	chr19:45681544-45681756	GM19238	blood:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
2	POLR2A	chr19:45681036-45683898	K562	blood:	n/a	n/a
3	TBP	chr19:45681058-45682273	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr19:45681600-45681750	GM12873	blood:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
5	FOXM1	chr19:45681196-45682337	GM12878	blood:	n/a	n/a
6	YY1	chr19:45681052-45683147	GM12878	blood:	n/a	n/a
7	CTCF	chr19:45681531-45681751	MCF-7	breast:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
8	CTCF	chr19:45681560-45681710	SAEC	small airway:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
9	CTCF	chr19:45681493-45681762	GM12892	blood:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
10	POLR2A	chr19:45681208-45682456	GM12878	blood:	n/a	n/a
11	CTCF	chr19:45681560-45681710	HCPEpiC	choroid plexus:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
12	CTCF	chr19:45681640-45681790	A549	lung:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
13	SIN3AK20	chr19:45681494-45681833	SK-N-SH	brain:	n/a	n/a
14	CCNT2	chr19:45681299-45682206	K562	blood:	n/a	n/a
15	CTCF	chr19:45681589-45681720	ProgFib	skin:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
16	FOS	chr19:45680982-45682029	MCF10A-Er-Src	breast:	n/a	chr19:45681985-45681994 chr19:45681607-45681616 chr19:45681807-45681821 chr19:45681520-45681529
17	REST	chr19:45680904-45682692	H1-neurons	neurons:	n/a	n/a
18	MAFK	chr19:45681338-45682092	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr19:45681620-45681770	HFF-Myc	foreskin:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
20	POLR2A	chr19:45681047-45682441	U87	brain:	n/a	n/a
21	POLR2A	chr19:45681296-45683092	K562	blood:	n/a	n/a
22	POLR2A	chr19:45680971-45682274	MCF10A-Er-Src	breast:	n/a	n/a
23	CEBPB	chr19:45681009-45682042	A549	lung:	n/a	n/a
24	EP300	chr19:45681467-45682205	GM12878	blood:	n/a	n/a
25	JUND	chr19:45681635-45681893	H1-hESC	embryonic stem cell:	n/a	chr19:45681807-45681821
26	YY1	chr19:45681080-45681729	K562	blood:	n/a	n/a
27	CTCF	chr19:45681640-45681790	HFF	foreskin:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
28	YY1	chr19:45681076-45681816	H1-hESC	embryonic stem cell:	n/a	n/a
29	IRF3	chr19:45681574-45682051	HepG2	liver:	n/a	chr19:45681658-45681672 chr19:45681602-45681616
30	CTCF	chr19:45681600-45681750	HL-60	blood:	n/a	chr19:45681650-45681668 chr19:45681652-45681673 chr19:45681651-45681667 chr19:45681655-45681665
31	SP1	chr19:45681160-45682960	GM12878	blood:	n/a	chr19:45681605-45681614 chr19:45681659-45681668 chr19:45681511-45681532 chr19:45681658-45681670 chr19:45681614-45681627 chr19:45681658-45681670 chr19:45681614-45681623 chr19:45681739-45681760 chr19:45681613-45681622 chr19:45681604-45681616 chr19:45681605-45681619 chr19:45681983-45682004 chr19:45681612-45681624 chr19:45681604-45681616 chr19:45681660-45681669 chr19:45681613-45681622 chr19:45681606-45681615
32	CHD2	chr19:45681300-45682227	K562	blood:	n/a	chr19:45681612-45681622
33	NFIC	chr19:45681080-45682202	HepG2	liver:	n/a	n/a
34	SIN3AK20	chr19:45681228-45682393	PFSK-1	brain:	n/a	n/a
35	USF1	chr19:45681421-45682354	HepG2	liver:	n/a	chr19:45681879-45681890 chr19:45682072-45682088
36	CEBPB	chr19:45681189-45682144	H1-hESC	embryonic stem cell:	n/a	n/a
37	RAD21	chr19:45681489-45681801	K562	blood:	n/a	chr19:45681651-45681670
38	USF2	chr19:45681454-45682440	Hela-S3	cervix:	n/a	chr19:45682072-45682088 chr19:45681879-45681890
39	HDAC2	chr19:45681513-45681800	K562	blood:	n/a	n/a
40	MXI1	chr19:45681014-45683063	GM12878	blood:	n/a	chr19:45681954-45681963
41	BHLHE40	chr19:45680931-45683148	K562	blood:	n/a	chr19:45682072-45682088
42	CEBPD	chr19:45681308-45681751	HepG2	liver:	n/a	n/a
43	CREB1	chr19:45680899-45682442	K562	blood:	n/a	n/a
44	SIN3AK20	chr19:45680879-45682979	MCF-7	breast:	n/a	n/a
45	RCOR1	chr19:45681154-45682303	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:45681125-45682363	H1-neurons	neurons:	n/a	n/a
47	MAX	chr19:45681088-45682737	SK-N-SH	brain:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
48	ZNF143	chr19:45681431-45682260	Hela-S3	cervix:	n/a	n/a
49	CREB1	chr19:45681002-45683025	GM12878	blood:	n/a	n/a
50	YY1	chr19:45681206-45681828	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45680180..45683713-chr19:45733323..45737109,3	K562	blood:
2	chr19:45658848..45663469-chr19:45680259..45684163,6	MCF-7	breast:
3	chr19:45581068..45583958-chr19:45681428..45684016,2	K562	blood:
4	chr17:16341750..16342479-chr19:45681510..45682384,2	Hela-S3	cervix:
5	chr19:45654421..45658397-chr19:45679888..45682724,3	K562	blood:
6	chr19:45644450..45646816-chr19:45679774..45683109,3	MCF-7	breast:
7	chr19:45662322..45663842-chr19:45681568..45683237,2	K562	blood:
8	chr19:45679504..45683518-chr19:45685241..45688488,5	MCF-7	breast:
9	chr19:45681420..45684587-chr19:45687242..45692393,7	MCF-7	breast:
10	chr19:45503982..45506844-chr19:45681115..45683310,3	K562	blood:
11	chr19:45662322..45668242-chr19:45680645..45684470,7	K562	blood:
12	chr19:45681162..45683480-chr19:45842144..45844672,3	K562	blood:
13	chr19:45680559..45684359-chr19:45688843..45692525,5	MCF-7	breast:
14	chr19:45655086..45657605-chr19:45680853..45682730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267545	TF binding region
BLOC1S3	TF binding region
TRAPPC6A	TF binding region
ENSG00000104892	Chromatin interaction
ENSG00000266958	Chromatin interaction
ENSG00000268341	Chromatin interaction
ENSG00000179846	Chromatin interaction
ENSG00000130201	Chromatin interaction
ENSG00000225157	Chromatin interaction
ENSG00000104856	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000175061	Chromatin interaction
ENSG00000104866	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	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1798099	chr19:45664218-45681988	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
9	esv1791796	chr19:45673701-45681988	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	esv1794498	chr19:45673701-45691040	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	esv1005203	chr19:45675812-45684868	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases
12	esv2422482	chr19:45676705-45769805	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	esv11492	chr19:45681508-45682018	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
14	esv1794901	chr19:45681661-45690775	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 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	chr19:45680200-45683200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:45680200-45684400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:45680400-45682200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:45680400-45682800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:45680400-45683200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:45680400-45683200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:45680400-45683200	Active TSS	GM12878-XiMat	blood
8	chr19:45680400-45683200	Active TSS	Hela-S3	cervix
9	chr19:45680400-45683400	Active TSS	H9 Cell Line	embryonic stem cell
10	chr19:45680400-45683600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:45680400-45683600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:45680400-45683600	Active TSS	K562	blood
13	chr19:45680400-45683800	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr19:45680600-45683000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:45680600-45683000	Active TSS	Osteobl	bone
16	chr19:45680600-45683200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:45680600-45683200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:45680600-45683200	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr19:45680600-45683200	Active TSS	Fetal Intestine Large	intestine
20	chr19:45680600-45683400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr19:45680600-45683400	Active TSS	Rectal Smooth Muscle	rectum
22	chr19:45680600-45683600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:45680600-45683600	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr19:45680600-45683600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:45680800-45682200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:45680800-45682400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:45680800-45682600	Active TSS	Fetal Kidney	kidney
28	chr19:45680800-45683000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:45680800-45683000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:45680800-45683000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:45680800-45683000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:45680800-45683000	Active TSS	Right Atrium	heart
33	chr19:45680800-45683200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr19:45680800-45683200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:45680800-45683200	Active TSS	Psoas Muscle	Psoas
36	chr19:45680800-45683200	Active TSS	NHDF-Ad	bronchial
37	chr19:45680800-45683200	Active TSS	NHLF	lung
38	chr19:45680800-45683400	Active TSS	Ovary	ovary
39	chr19:45680800-45683600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr19:45681000-45682000	Active TSS	Brain Germinal Matrix	brain
41	chr19:45681000-45682200	Active TSS	Colonic Mucosa	Colon
42	chr19:45681000-45682200	Active TSS	Fetal Muscle Trunk	muscle
43	chr19:45681000-45682400	Active TSS	Placenta Amnion	Placenta Amnion
44	chr19:45681000-45682600	Active TSS	Pancreas	Pancrea
45	chr19:45681000-45682600	Bivalent/Poised TSS	HepG2	liver
46	chr19:45681000-45682800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:45681000-45682800	Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr19:45681000-45682800	Active TSS	Right Ventricle	heart
49	chr19:45681000-45682800	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr19:45681000-45683000	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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