Variant report

Variant	rs140607687
Chromosome Location	chr19:42580211-42580212
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	IRF1	chr19:42579302-42580510	K562	blood:	n/a	chr19:42580241-42580250 chr19:42579506-42579515 chr19:42579737-42579749 chr19:42579805-42579818 chr19:42579736-42579750 chr19:42579738-42579748 chr19:42579737-42579749 chr19:42579805-42579818 chr19:42579804-42579815 chr19:42579806-42579816 chr19:42579736-42579756 chr19:42579805-42579818 chr19:42579736-42579749 chr19:42579805-42579816 chr19:42579734-42579748 chr19:42579805-42579819 chr19:42579806-42579820 chr19:42579804-42579818
2	MAX	chr19:42580170-42580637	K562	blood:	n/a	chr19:42580285-42580295
3	CREB1	chr19:42579617-42580487	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr19:42579866-42580395	Hela-S3	cervix:	n/a	chr19:42580364-42580374
5	POLR2A	chr19:42578647-42580693	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:42580156-42580598	K562	blood:	n/a	n/a
7	MAX	chr19:42579179-42580895	H1-hESC	embryonic stem cell:	n/a	chr19:42580818-42580827 chr19:42580818-42580828 chr19:42580819-42580826 chr19:42580285-42580295
8	SIX5	chr19:42579595-42580376	A549	lung:	n/a	n/a
9	PML	chr19:42579006-42580719	GM12878	blood:	n/a	n/a
10	PML	chr19:42579605-42580633	MCF-7	breast:	n/a	n/a
11	TAF1	chr19:42579232-42580589	A549	lung:	n/a	n/a
12	YY1	chr19:42579545-42580445	HCT-116	colon:	n/a	chr19:42579948-42579970 chr19:42580000-42580014 chr19:42579965-42579979 chr19:42579952-42579972 chr19:42580266-42580277 chr19:42579959-42579967
13	POLR2A	chr19:42578705-42580546	GM12891	blood:	n/a	n/a
14	MAX	chr19:42579299-42580450	SK-N-SH	brain:	n/a	chr19:42580285-42580295
15	POLR2A	chr19:42579728-42580601	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:42579046-42580623	GM19193	blood:	n/a	n/a
17	POLR2A	chr19:42578660-42580906	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:42579678-42580804	HUVEC	blood vessel:	n/a	n/a
19	PAX5	chr19:42580121-42580482	GM12878	blood:	n/a	chr19:42580449-42580458
20	NFYA	chr19:42579907-42580507	K562	blood:	n/a	chr19:42580208-42580220 chr19:42580204-42580219 chr19:42580241-42580253 chr19:42580200-42580218 chr19:42580205-42580219
21	MAX	chr19:42579507-42580928	ECC-1	luminal epithelium:	n/a	chr19:42580818-42580827 chr19:42580818-42580828 chr19:42580819-42580826 chr19:42580285-42580295
22	FOS	chr19:42579912-42580420	GM12878	blood:	n/a	n/a
23	MAX	chr19:42579469-42580289	MCF-7	breast:	n/a	n/a
24	BHLHE40	chr19:42579796-42580849	HepG2	liver:	n/a	n/a
25	CEBPD	chr19:42580207-42580429	HepG2	liver:	n/a	n/a
26	MYC	chr19:42579372-42580979	MCF10A-Er-Src	breast:	n/a	chr19:42580818-42580827 chr19:42580818-42580828 chr19:42580819-42580826 chr19:42580285-42580295
27	POLR2A	chr19:42578770-42580593	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:42578640-42580546	HCT-116	colon:	n/a	n/a
29	TBP	chr19:42579222-42580822	K562	blood:	n/a	n/a
30	HMGN3	chr19:42579804-42580778	K562	blood:	n/a	n/a
31	MAX	chr19:42579299-42580582	ECC-1	luminal epithelium:	n/a	chr19:42580285-42580295
32	FOS	chr19:42579871-42580285	MCF10A-Er-Src	breast:	n/a	n/a
33	MXI1	chr19:42578604-42581499	SK-N-SH	brain:	n/a	chr19:42580819-42580828
34	POLR2A	chr19:42579159-42580982	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr19:42579290-42580850	GM12878	blood:	n/a	chr19:42580818-42580827 chr19:42580818-42580828 chr19:42580819-42580826 chr19:42580285-42580295
36	MYC	chr19:42580042-42580426	HUVEC	blood vessel:	n/a	chr19:42580285-42580295
37	STAT3	chr19:42580211-42580378	MCF10A-Er-Src	breast:	n/a	n/a
38	ELF1	chr19:42579648-42580544	MCF-7	breast:	n/a	chr19:42580002-42580014 chr19:42580457-42580469
39	MYC	chr19:42579263-42580959	K562	blood:	n/a	chr19:42580818-42580827 chr19:42580818-42580828 chr19:42580819-42580826 chr19:42580285-42580295
40	RFX5	chr19:42579069-42581234	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr19:42578954-42580813	K562	blood:	n/a	n/a
42	POLR2A	chr19:42579632-42580998	H1-neurons	neurons:	n/a	n/a
43	CREB1	chr19:42579224-42580615	GM12878	blood:	n/a	n/a
44	TAF1	chr19:42579333-42580741	K562	blood:	n/a	n/a
45	MAX	chr19:42579006-42581001	K562	blood:	n/a	chr19:42580818-42580827 chr19:42580818-42580828 chr19:42580819-42580826 chr19:42580285-42580295
46	POLR2A	chr19:42579211-42580575	H1-hESC	embryonic stem cell:	n/a	n/a
47	ELF1	chr19:42579767-42580490	K562	blood:	n/a	chr19:42580002-42580014 chr19:42580457-42580469
48	CREB1	chr19:42579784-42580472	A549	lung:	n/a	n/a
49	POLR2A	chr19:42579234-42580740	NB4	blood:	n/a	n/a
50	HEY1	chr19:42579146-42580687	HepG2	liver:	n/a	chr19:42580579-42580594 chr19:42579975-42579990 chr19:42579966-42579981

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:42580205-42580255	GM12891	blood:	n/a
2	chr19:42580205-42580255	IMR90	lung:	fetal
3	chr19:42580165-42580215	NH-A	brain:	n/a
4	chr19:42580165-42580215	SK-N-MC	brain:	n/a
5	chr19:42580205-42580255	PFSK-1	brain:	n/a
6	chr19:42580205-42580255	SK-N-SH	brain:	n/a
7	chr19:42580165-42580215	RPTEC	kidney:	n/a
8	chr19:42580205-42580255	AG09319	gingival:	n/a
9	chr19:42580165-42580215	SAEC	small airway:	n/a
10	chr19:42580205-42580255	NT2-D1	testis:	n/a
11	chr19:42580205-42580255	CMK	blood:	n/a
12	chr19:42580205-42580255	H1-hESC	embryonic stem cell:	embryo
13	chr19:42580165-42580215	HCPEpiC	choroid plexus:	n/a
14	chr19:42580205-42580255	NHDF-neo	bronchial:	n/a
15	chr19:42580205-42580255	Hepatocyte	liver:	n/a
16	chr19:42580165-42580215	Hepatocyte	liver:	n/a
17	chr19:42580205-42580255	Hela-S3	cervix:	n/a
18	chr19:42580165-42580215	PFSK-1	brain:	n/a
19	chr19:42580205-42580255	GM19239	blood:	n/a
20	chr19:42580205-42580255	HCF	heart:	n/a
21	chr19:42580205-42580255	HMEC	breast:	n/a
22	chr19:42580205-42580255	ovcar-3	ovarian:	n/a
23	chr19:42580165-42580215	HL-60	blood:	n/a
24	chr19:42580165-42580215	Caco-2	colon:	n/a
25	chr19:42580205-42580255	NHBE	bronchial:	n/a
26	chr19:42580205-42580255	HIPEpiC	eye:	n/a
27	chr19:42580205-42580255	AG10803	skin:	n/a
28	chr19:42580165-42580215	AG09319	gingival:	n/a
29	chr19:42580205-42580255	ProgFib	skin:	n/a
30	chr19:42580165-42580215	GM06990	blood:	n/a
31	chr19:42580205-42580255	PANC-1	pancreas:	n/a
32	chr19:42580165-42580215	HRPEpiC	eye:	n/a
33	chr19:42580165-42580215	HEK293	kidney:	embryo
34	chr19:42580165-42580215	SK-N-SH	brain:	n/a
35	chr19:42580205-42580255	MCF10A-Er-Src	breast:	n/a
36	chr19:42580205-42580255	HRPEpiC	eye:	n/a
37	chr19:42580205-42580255	AG04449	skin:	fetal
38	chr19:42580165-42580215	GM12891	blood:	n/a
39	chr19:42580165-42580215	AG04450	lung:	fetal
40	chr19:42580165-42580215	HCT-116	colon:	n/a
41	chr19:42580205-42580255	T-47D	breast:	n/a
42	chr19:42580165-42580215	MCF-7	breast:	n/a
43	chr19:42580165-42580215	HMEC	breast:	n/a
44	chr19:42580205-42580255	HCPEpiC	choroid plexus:	n/a
45	chr19:42580165-42580215	HNPCEpiC	eye:	n/a
46	chr19:42580205-42580255	GM06990	blood:	n/a
47	chr19:42580165-42580215	HUVEC	blood vessel:	n/a
48	chr19:42580165-42580215	HAEpiC	amniotic membrane:	n/a
49	chr19:42580205-42580255	Jurkat	blood:	n/a
50	chr19:42580165-42580215	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42362719..42367011-chr19:42578185..42581831,5	K562	blood:
2	chr19:42578256..42580709-chr19:42719856..42723017,3	MCF-7	breast:
3	chr19:42579835..42581809-chr19:42805426..42808329,2	K562	blood:
4	chr19:42580132..42580730-chrX:154444608..154445569,2	NB4	blood:
5	chr19:42579420..42580323-chr6:86388195..86389033,2	NB4	blood:
6	chr1:149858185..149858712-chr19:42579689..42580587,2	Hela-S3	cervix:
7	chr19:42579143..42581676-chr19:42599537..42601981,2	K562	blood:
8	chr17:48450185..48450888-chr19:42579497..42580216,2	HCT-116	colon:
9	chr19:42579446..42580287-chr20:21283218..21284033,2	HCT-116	colon:
10	chr19:42362767..42365637-chr19:42577892..42581321,5	K562	blood:
11	chr19:42460531..42463518-chr19:42578179..42580939,2	K562	blood:
12	chr19:42362802..42365669-chr19:42579542..42583856,4	MCF-7	breast:
13	chr19:42578926..42581417-chr19:42757384..42759123,2	K562	blood:
14	chr19:42501468..42504602-chr19:42578170..42581487,3	K562	blood:
15	chr19:42462261..42465397-chr19:42579731..42582911,4	MCF-7	breast:
16	chr19:42386135..42388674-chr19:42579222..42581788,5	K562	blood:
17	chr19:42570275..42573943-chr19:42577525..42580461,7	K562	blood:
18	chr19:42386135..42388460-chr19:42579140..42581462,3	K562	blood:
19	chr19:42579405..42581484-chr19:42787067..42789919,2	K562	blood:
20	chr19:42388358..42390538-chr19:42579521..42581745,2	MCF-7	breast:
21	chr19:42568861..42574784-chr19:42577207..42582012,11	K562	blood:
22	chr19:42460466..42464604-chr19:42577075..42581382,5	MCF-7	breast:

Variant related genes	Relation type
ZNF574	TF binding region
ZNF574	CpG island
ENSG00000184260	Chromatin interaction
ENSG00000105409	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000088930	Chromatin interaction
ENSG00000028277	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105732	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000105737	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000160570	Chromatin interaction
ENSG00000154920	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000155959	Chromatin interaction
ENSG00000105372	Chromatin interaction
ENSG00000108826	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv911783	chr19:42575462-42624662	Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv12493	chr19:42579999-42582314	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	n/a
7	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 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	chr19:42578800-42581600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:42579000-42581000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:42579000-42581400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:42579000-42582000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:42579000-42582200	Active TSS	HSMM	muscle
6	chr19:42579000-42582600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:42579200-42580800	Transcr. at gene 5' and 3'	Right Atrium	heart
8	chr19:42579200-42581000	Active TSS	Colon Smooth Muscle	Colon
9	chr19:42579200-42581000	Active TSS	Fetal Kidney	kidney
10	chr19:42579200-42581200	Active TSS	Psoas Muscle	Psoas
11	chr19:42579200-42581400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr19:42579200-42581400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:42579200-42581600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr19:42579200-42581800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:42579200-42582000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr19:42579200-42582000	Active TSS	HSMMtube	muscle
17	chr19:42579400-42580800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:42579400-42580800	Active TSS	Stomach Mucosa	stomach
19	chr19:42579400-42581000	Active TSS	Right Ventricle	heart
20	chr19:42579400-42581000	Active TSS	Small Intestine	intestine
21	chr19:42579400-42581200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:42579400-42581200	Active TSS	Aorta	Aorta
23	chr19:42579400-42581200	Active TSS	Fetal Intestine Large	intestine
24	chr19:42579400-42581200	Active TSS	Fetal Intestine Small	intestine
25	chr19:42579400-42581200	Active TSS	Fetal Lung	lung
26	chr19:42579400-42581200	Active TSS	Gastric	stomach
27	chr19:42579400-42581200	Active TSS	Ovary	ovary
28	chr19:42579400-42581200	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr19:42579400-42581400	Active TSS	Esophagus	oesophagus
30	chr19:42579600-42580400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:42579600-42580400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:42579600-42580600	Active TSS	Primary B cells from cord blood	blood
33	chr19:42579600-42580800	Active TSS	Primary monocytes fromperipheralblood	blood
34	chr19:42579600-42580800	Active TSS	Primary T cells from cord blood	blood
35	chr19:42579600-42580800	Active TSS	Primary hematopoietic stem cells	blood
36	chr19:42579600-42580800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:42579600-42580800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:42579600-42580800	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr19:42579600-42580800	Active TSS	Liver	Liver
40	chr19:42579600-42580800	Active TSS	Brain Hippocampus Middle	brain
41	chr19:42579600-42580800	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr19:42579600-42580800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:42579600-42580800	Active TSS	Duodenum Mucosa	Duodenum
44	chr19:42579600-42580800	Active TSS	Placenta Amnion	Placenta Amnion
45	chr19:42579600-42580800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr19:42579600-42580800	Active TSS	Rectal Smooth Muscle	rectum
47	chr19:42579600-42580800	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr19:42579600-42580800	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr19:42579600-42580800	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr19:42579600-42581000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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