Variant report

Variant	rs549762963
Chromosome Location	chr19:52693111-52693112
allele	A/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	NR2F2	chr19:52692654-52693588	K562	blood:	n/a	n/a
2	STAT1	chr19:52692737-52693807	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:52693073-52693755	K562	blood:	n/a	n/a
4	TAF1	chr19:52693082-52693620	GM12891	blood:	n/a	n/a
5	ETS1	chr19:52692637-52693890	A549	lung:	n/a	chr19:52693076-52693091
6	GATA3	chr19:52693088-52693775	T-47D	breast:	n/a	chr19:52693555-52693562 chr19:52693554-52693564 chr19:52693555-52693564 chr19:52693555-52693562 chr19:52693555-52693562
7	SPI1	chr19:52692914-52693359	GM12891	blood:	n/a	chr19:52693079-52693092 chr19:52693080-52693089 chr19:52693266-52693279 chr19:52693078-52693091
8	MAX	chr19:52692569-52694037	A549	lung:	n/a	chr19:52693618-52693628 chr19:52693289-52693299 chr19:52693254-52693263
9	MXI1	chr19:52692258-52693773	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr19:52693107-52693839	HepG2	liver:	n/a	n/a
11	STAT3	chr19:52692681-52693178	GM12878	blood:	n/a	n/a
12	GABPA	chr19:52692586-52693789	SK-N-SH	brain:	n/a	chr19:52693665-52693674 chr19:52692927-52692938 chr19:52692927-52692941 chr19:52693082-52693089
13	CBX3	chr19:52693023-52693563	K562	blood:	n/a	n/a
14	MYC	chr19:52692784-52693727	MCF-7	breast:	n/a	chr19:52693618-52693628 chr19:52693289-52693299 chr19:52693254-52693263
15	NFYA	chr19:52692612-52694060	Hela-S3	cervix:	n/a	chr19:52693132-52693147 chr19:52692994-52693007 chr19:52693209-52693224 chr19:52692992-52693007 chr19:52693131-52693143 chr19:52692992-52693007 chr19:52692993-52693007 chr19:52692995-52693005 chr19:52692995-52693005
16	MYC	chr19:52693111-52693450	HUVEC	blood vessel:	n/a	chr19:52693289-52693299 chr19:52693254-52693263
17	YY1	chr19:52692980-52694093	A549	lung:	n/a	chr19:52693751-52693760 chr19:52693339-52693359
18	MAZ	chr19:52692230-52693947	GM12878	blood:	n/a	chr19:52693618-52693628 chr19:52693289-52693299 chr19:52693254-52693263
19	TAF1	chr19:52693107-52693805	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:52692552-52693983	MCF-7	breast:	n/a	n/a
21	NFIC	chr19:52692271-52693629	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr19:52692596-52694094	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:52692067-52694881	GM12891	blood:	n/a	n/a
24	TBP	chr19:52692269-52693507	Hela-S3	cervix:	n/a	n/a
25	MXI1	chr19:52692867-52693846	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:52692324-52694327	GM15510	blood:	n/a	n/a
27	STAT3	chr19:52692958-52693345	MCF10A-Er-Src	breast:	n/a	n/a
28	HEY1	chr19:52693108-52693830	K562	blood:	n/a	n/a
29	YY1	chr19:52693088-52693726	GM12892	blood:	n/a	chr19:52693339-52693359
30	POLR2A	chr19:52692475-52694195	IMR90	lung:	n/a	n/a
31	SP1	chr19:52692714-52693829	H1-hESC	embryonic stem cell:	n/a	chr19:52692985-52693006 chr19:52693150-52693164 chr19:52693133-52693154 chr19:52693618-52693627 chr19:52693614-52693628 chr19:52693259-52693270 chr19:52693153-52693165 chr19:52692807-52692821 chr19:52693617-52693629 chr19:52693153-52693165 chr19:52693210-52693231 chr19:52693617-52693629
32	FOXP2	chr19:52693086-52693801	PFSK-1	brain:	n/a	n/a
33	ELF1	chr19:52692791-52693719	HepG2	liver:	n/a	chr19:52693080-52693089
34	JUND	chr19:52692670-52693889	A549	lung:	n/a	n/a
35	RFX5	chr19:52692755-52693747	GM12878	blood:	n/a	chr19:52692995-52693004
36	TBL1XR1	chr19:52692665-52693753	K562	blood:	n/a	n/a
37	CREB1	chr19:52692458-52693976	HepG2	liver:	n/a	n/a
38	POLR2A	chr19:52692655-52694313	GM12892	blood:	n/a	n/a
39	GABPA	chr19:52692701-52693693	A549	lung:	n/a	chr19:52693665-52693674 chr19:52692927-52692938 chr19:52692927-52692941 chr19:52693082-52693089
40	ARID3A	chr19:52692734-52693274	K562	blood:	n/a	n/a
41	POLR2A	chr19:52692443-52694254	K562	blood:	n/a	n/a
42	POLR2A	chr19:52692655-52693825	GM10847	blood:	n/a	n/a
43	SP4	chr19:52692877-52693874	H1-hESC	embryonic stem cell:	n/a	chr19:52693151-52693167 chr19:52693259-52693270 chr19:52693149-52693165
44	SIN3AK20	chr19:52692117-52694086	MCF-7	breast:	n/a	n/a
45	ELK1	chr19:52692799-52693753	K562	blood:	n/a	n/a
46	CTCF	chr19:52692692-52693457	GM12878	blood:	n/a	n/a
47	MAX	chr19:52693108-52693805	K562	blood:	n/a	chr19:52693618-52693628 chr19:52693289-52693299 chr19:52693254-52693263
48	ELF1	chr19:52692348-52693998	GM12878	blood:	n/a	chr19:52693080-52693089
49	POLR2A	chr19:52692031-52693988	H1-hESC	embryonic stem cell:	n/a	n/a
50	FOXM1	chr19:52692507-52694034	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52693064-52693114	Jurkat	blood:	n/a
2	chr19:52693064-52693114	HAEpiC	amniotic membrane:	n/a
3	chr19:52693064-52693114	HMEC	breast:	n/a
4	chr19:52693064-52693114	ECC-1	luminal epithelium:	n/a
5	chr19:52693064-52693114	AG09309	skin:	n/a
6	chr19:52693064-52693114	Hepatocyte	liver:	n/a
7	chr19:52693064-52693114	AG10803	skin:	n/a
8	chr19:52693064-52693114	GM12891	blood:	n/a
9	chr19:52693064-52693114	HCT-116	colon:	n/a
10	chr19:52693064-52693114	HEK293	kidney:	embryo
11	chr19:52693064-52693114	HIPEpiC	eye:	n/a
12	chr19:52693064-52693114	T-47D	breast:	n/a
13	chr19:52693064-52693114	RPTEC	kidney:	n/a
14	chr19:52693064-52693114	SK-N-SH	brain:	n/a
15	chr19:52693064-52693114	CMK	blood:	n/a
16	chr19:52693064-52693114	NH-A	brain:	n/a
17	chr19:52693064-52693114	LNCaP	prostate:	n/a
18	chr19:52693064-52693114	HCPEpiC	choroid plexus:	n/a
19	chr19:52693064-52693114	NHBE	bronchial:	n/a
20	chr19:52693064-52693114	ovcar-3	ovarian:	n/a
21	chr19:52693064-52693114	NT2-D1	testis:	n/a
22	chr19:52693064-52693114	AoSMC	blood vessel:	n/a
23	chr19:52693064-52693114	HRE	kidney:	n/a
24	chr19:52693064-52693114	SKMC	muscle:	n/a
25	chr19:52693064-52693114	ProgFib	skin:	n/a
26	chr19:52693064-52693114	U87	brain:	n/a
27	chr19:52693064-52693114	IMR90	lung:	fetal
28	chr19:52693064-52693114	H1-hESC	embryonic stem cell:	embryo
29	chr19:52693064-52693114	HEEpiC	esophagus:	n/a
30	chr19:52693064-52693114	Caco-2	colon:	n/a
31	chr19:52693064-52693114	SK-N-MC	brain:	n/a
32	chr19:52693064-52693114	SK-N-SH_RA	brain:	n/a
33	chr19:52693064-52693114	HCF	heart:	n/a
34	chr19:52693064-52693114	PrEC	prostate:	n/a
35	chr19:52693064-52693114	MCF10A-Er-Src	breast:	n/a
36	chr19:52693064-52693114	GM06990	blood:	n/a
37	chr19:52693064-52693114	MCF-7	breast:	n/a
38	chr19:52693064-52693114	GM19239	blood:	n/a
39	chr19:52693064-52693114	NB4	blood:	n/a
40	chr19:52693064-52693114	BE2_C	brain:	n/a
41	chr19:52693064-52693114	Hela-S3	cervix:	n/a
42	chr19:52693064-52693114	HepG2	liver:	n/a
43	chr19:52693064-52693114	SAEC	small airway:	n/a
44	chr19:52693064-52693114	PANC-1	pancreas:	n/a
45	chr19:52693064-52693114	HPAEpiC	pulmonary alveolar:	n/a
46	chr19:52693064-52693114	AG09319	gingival:	n/a
47	chr19:52693064-52693114	NHDF-neo	bronchial:	n/a
48	chr19:52693064-52693114	HL-60	blood:	n/a
49	chr19:52693064-52693114	HRCEpiC	kidney:	n/a
50	chr19:52693064-52693114	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr19:52641405..52644253-chr19:52691691..52696539,6	MCF-7	breast:
2	chr19:52692900..52696088-chr19:52702014..52707428,7	MCF-7	breast:
3	chr19:52598726..52600984-chr19:52691577..52693709,2	MCF-7	breast:
4	chr19:52597423..52599077-chr19:52692134..52694986,2	K562	blood:
5	chr1:17221697..17224418-chr19:52692331..52695072,2	MCF-7	breast:
6	chr19:52641479..52644491-chr19:52690575..52695402,7	MCF-7	breast:
7	chr19:52641692..52643573-chr19:52692556..52694474,2	K562	blood:
8	chr19:52692960..52694798-chr19:52714697..52716755,2	K562	blood:
9	chr19:52671404..52675593-chr19:52690586..52694996,6	MCF-7	breast:
10	chr19:52691967..52694543-chr19:52715939..52718199,3	MCF-7	breast:
11	chr19:52691998..52694919-chr19:53605403..53608321,3	K562	blood:
12	chr19:52692325..52695090-chr19:52733176..52735417,3	MCF-7	breast:
13	chr19:52677704..52680219-chr19:52691425..52693169,2	MCF-7	breast:

Variant related genes	Relation type
PPP2R1A	TF binding region
PPP2R1A	CpG island
ENSG00000268015	Chromatin interaction
ENSG00000170949	Chromatin interaction
ENSG00000256087	Chromatin interaction
ENSG00000267827	Chromatin interaction
ENSG00000196267	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000267927	Chromatin interaction
ENSG00000207005	Chromatin interaction
ENSG00000197608	Chromatin interaction
ENSG00000105568	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv580007	chr19:52660279-52693277	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv21017	chr19:52692555-52696215	Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 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	chr19:52691600-52694600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:52691800-52694400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:52691800-52694600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:52691800-52694600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:52692000-52694200	Active TSS	Right Atrium	heart
6	chr19:52692000-52694400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:52692000-52694400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:52692000-52694400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:52692000-52694400	Active TSS	Psoas Muscle	Psoas
10	chr19:52692000-52694600	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr19:52692000-52694600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr19:52692000-52694800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:52692000-52694800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:52692000-52695400	Active TSS	Left Ventricle	heart
15	chr19:52692200-52693800	Active TSS	HepG2	liver
16	chr19:52692200-52694200	Active TSS	Gastric	stomach
17	chr19:52692200-52694400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr19:52692200-52694400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:52692200-52694400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:52692200-52694400	Active TSS	Aorta	Aorta
21	chr19:52692200-52694400	Active TSS	Esophagus	oesophagus
22	chr19:52692200-52694600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr19:52692200-52694600	Active TSS	GM12878-XiMat	blood
24	chr19:52692200-52694800	Active TSS	Lung	lung
25	chr19:52692200-52694800	Active TSS	Ovary	ovary
26	chr19:52692400-52693600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:52692400-52694000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:52692400-52694000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:52692400-52694000	Active TSS	Thymus	Thymus
30	chr19:52692400-52694200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:52692400-52694200	Active TSS	Liver	Liver
32	chr19:52692400-52694200	Active TSS	Brain Angular Gyrus	brain
33	chr19:52692400-52694200	Active TSS	Brain Cingulate Gyrus	brain
34	chr19:52692400-52694200	Active TSS	Brain Germinal Matrix	brain
35	chr19:52692400-52694200	Active TSS	Brain Substantia Nigra	brain
36	chr19:52692400-52694200	Active TSS	Colonic Mucosa	Colon
37	chr19:52692400-52694200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:52692400-52694200	Active TSS	Fetal Brain Male	brain
39	chr19:52692400-52694200	Active TSS	Pancreas	Pancrea
40	chr19:52692400-52694200	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr19:52692400-52694200	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr19:52692400-52694200	Active TSS	Rectal Smooth Muscle	rectum
43	chr19:52692400-52694400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:52692400-52694400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr19:52692400-52694400	Active TSS	Brain Anterior Caudate	brain
46	chr19:52692400-52694400	Active TSS	Duodenum Mucosa	Duodenum
47	chr19:52692400-52694400	Active TSS	Fetal Brain Female	brain
48	chr19:52692400-52694400	Active TSS	Fetal Kidney	kidney
49	chr19:52692400-52694400	Active TSS	Fetal Lung	lung
50	chr19:52692400-52694400	Active TSS	Fetal Stomach	stomach

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