Variant report

Variant	rs28377509
Chromosome Location	chr19:55670825-55670826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55670283-55671120	HCT-116	colon:	n/a	n/a
2	POLR2A	chr19:55670428-55671094	U87	brain:	n/a	n/a
3	PML	chr19:55670143-55670866	K562	blood:	n/a	n/a
4	CEBPB	chr19:55670250-55671004	Hela-S3	cervix:	n/a	n/a
5	BHLHE40	chr19:55670115-55671001	K562	blood:	n/a	n/a
6	MAX	chr19:55670244-55670946	K562	blood:	n/a	n/a
7	POLR2A	chr19:55670284-55671084	Hela-S3	cervix:	n/a	n/a
8	MEF2A	chr19:55670135-55670902	K562	blood:	n/a	n/a
9	THAP1	chr19:55670455-55671022	K562	blood:	n/a	n/a
10	CCNT2	chr19:55670232-55670848	K562	blood:	n/a	n/a
11	POLR2A	chr19:55670399-55670911	U87	brain:	n/a	n/a
12	ZBTB7A	chr19:55670268-55670921	K562	blood:	n/a	n/a
13	NR2F2	chr19:55669889-55671122	K562	blood:	n/a	n/a
14	SMC3	chr19:55670301-55670950	Hela-S3	cervix:	n/a	n/a
15	HMGN3	chr19:55670314-55670948	K562	blood:	n/a	n/a
16	FOS	chr19:55670334-55670964	MCF10A-Er-Src	breast:	n/a	n/a
17	ZC3H11A	chr19:55669949-55670921	K562	blood:	n/a	n/a
18	UBTF	chr19:55670278-55670987	K562	blood:	n/a	n/a
19	ZNF263	chr19:55670350-55671184	HEK293-T-REx	kidney:	n/a	n/a
20	ELF1	chr19:55670315-55670835	K562	blood:	n/a	n/a
21	MAZ	chr19:55670374-55671055	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:55670361-55671148	HCT-116	colon:	n/a	n/a
23	CBX3	chr19:55670181-55671008	K562	blood:	n/a	n/a
24	MXI1	chr19:55670232-55670881	K562	blood:	n/a	n/a
25	RCOR1	chr19:55669930-55671069	K562	blood:	n/a	n/a
26	POLR2A	chr19:55669988-55671339	K562	blood:	n/a	n/a
27	TEAD4	chr19:55669783-55670983	K562	blood:	n/a	n/a
28	JUN	chr19:55669767-55672364	K562	blood:	n/a	chr19:55672186-55672195
29	POLR2A	chr19:55670428-55671095	U87	brain:	n/a	n/a
30	MYC	chr19:55670137-55670830	K562	blood:	n/a	n/a
31	IRF1	chr19:55670176-55670830	K562	blood:	n/a	n/a
32	POLR2A	chr19:55670215-55671096	K562	blood:	n/a	n/a
33	POLR2A	chr19:55670450-55670951	PFSK-1	brain:	n/a	n/a
34	JUND	chr19:55670045-55671019	K562	blood:	n/a	n/a
35	UBTF	chr19:55670110-55670954	K562	blood:	n/a	n/a
36	MAX	chr19:55670295-55670834	K562	blood:	n/a	n/a
37	GABPA	chr19:55670357-55670850	K562	blood:	n/a	n/a
38	MAX	chr19:55670228-55671102	K562	blood:	n/a	n/a
39	FOSL2	chr19:55670627-55671092	A549	lung:	n/a	n/a
40	POLR2A	chr19:55670220-55670876	K562	blood:	n/a	n/a
41	TEAD4	chr19:55669742-55670983	K562	blood:	n/a	n/a
42	JUN	chr19:55670175-55670926	Hela-S3	cervix:	n/a	n/a
43	RCOR1	chr19:55670261-55670998	Hela-S3	cervix:	n/a	n/a
44	TCF7L2	chr19:55670371-55670953	Hela-S3	cervix:	n/a	n/a
45	FOS	chr19:55670265-55670941	MCF10A-Er-Src	breast:	n/a	n/a
46	MAZ	chr19:55669787-55670981	K562	blood:	n/a	n/a
47	RCOR1	chr19:55669957-55670916	K562	blood:	n/a	n/a
48	ETS1	chr19:55670217-55670961	K562	blood:	n/a	n/a
49	POLR2A	chr19:55670228-55670845	K562	blood:	n/a	n/a
50	FOS	chr19:55670824-55670973	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55669739..55671839-chr19:55895942..55898733,2	K562	blood:
2	chr19:55670339..55672194-chr19:55895106..55898791,3	K562	blood:
3	chr19:55650102..55652468-chr19:55670117..55672433,2	K562	blood:
4	chr19:55652319..55652850-chr19:55670517..55671151,2	K562	blood:
5	chr19:55656068..55658188-chr19:55669727..55672257,4	K562	blood:
6	chr19:55598098..55602192-chr19:55668353..55672028,4	K562	blood:
7	chr19:55669904..55673815-chr19:55917688..55921815,5	K562	blood:
8	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
9	chr19:55658387..55665037-chr19:55666866..55670836,8	K562	blood:
10	chr19:55670803..55672973-chr19:55678461..55680015,2	MCF-7	breast:
11	chr19:55669094..55672573-chr19:55676633..55678240,3	K562	blood:
12	chr19:55590282..55593983-chr19:55668450..55672239,5	K562	blood:
13	chr19:55624850..55627348-chr19:55669347..55671433,3	K562	blood:
14	chr19:55573018..55574580-chr19:55668896..55671784,2	K562	blood:
15	chr19:55669654..55671920-chr19:55893818..55896729,2	MCF-7	breast:
16	chr19:55657720..55659447-chr19:55670409..55672561,2	MCF-7	breast:
17	chr19:55670813..55674787-chr19:55917654..55919984,3	MCF-7	breast:
18	chr19:55656783..55658511-chr19:55670096..55672623,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55670790-55671356	ENSG00000249659

No data

Variant related genes	Relation type
TNNI3	TF binding region
ENSG00000233493	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000160439	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000105048	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10418024	0.89[EUR][1000 genomes]
rs10422172	0.92[ASN][1000 genomes]
rs10422978	0.89[EUR][1000 genomes]
rs11667847	0.86[EUR][1000 genomes]
rs11671293	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729836	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729838	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786866	0.85[ASN][1000 genomes]
rs3848619	0.91[ASN][1000 genomes]
rs6509933	0.93[ASN][1000 genomes]
rs891187	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55668600-55671600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:55668600-55672000	Weak transcription	Pancreas	Pancrea
3	chr19:55668800-55671600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:55669000-55672000	Weak transcription	Spleen	Spleen
5	chr19:55669000-55672800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
6	chr19:55669200-55672200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:55669200-55672800	Enhancers	Fetal Heart	heart
8	chr19:55669600-55672400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr19:55669600-55673400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr19:55669800-55671600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr19:55669800-55672000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:55669800-55672400	Enhancers	A549	lung
13	chr19:55670000-55671000	Enhancers	Psoas Muscle	Psoas
14	chr19:55670000-55671000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
15	chr19:55670000-55671600	Enhancers	Placenta	Placenta
16	chr19:55670000-55672000	Flanking Active TSS	K562	blood
17	chr19:55670000-55672200	Flanking Active TSS	Hela-S3	cervix
18	chr19:55670000-55672400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:55670200-55671000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:55670200-55671200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:55670200-55671800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:55670200-55671800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:55670200-55672000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr19:55670200-55672000	Enhancers	Primary hematopoietic stem cells	blood
25	chr19:55670400-55671000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:55670400-55671000	Bivalent Enhancer	Ovary	ovary
27	chr19:55670400-55671000	Bivalent Enhancer	HepG2	liver
28	chr19:55670400-55671200	Enhancers	Duodenum Mucosa	Duodenum
29	chr19:55670400-55671200	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr19:55670400-55671200	Bivalent Enhancer	Stomach Mucosa	stomach
31	chr19:55670400-55671400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:55670400-55671600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:55670400-55671600	Enhancers	NHLF	lung
34	chr19:55670400-55671800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr19:55670400-55671800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr19:55670400-55671800	Enhancers	HSMMtube	muscle
37	chr19:55670400-55672000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:55670400-55672000	Enhancers	HMEC	breast
39	chr19:55670400-55672000	Flanking Active TSS	NHEK	skin
40	chr19:55670400-55672200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
41	chr19:55670400-55672400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:55670400-55672400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr19:55670600-55671000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr19:55670600-55671000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr19:55670600-55671000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
46	chr19:55670600-55671000	Bivalent Enhancer	Fetal Stomach	stomach
47	chr19:55670600-55671000	Flanking Active TSS	Left Ventricle	heart
48	chr19:55670600-55671000	Enhancers	NHDF-Ad	bronchial
49	chr19:55670600-55671200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:55670600-55671600	Active TSS	Right Atrium	heart

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