Variant report

Variant	rs2657928
Chromosome Location	chr19:52773078-52773079
allele	A/G
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	E2F6	chr19:52772530-52773429	A549	lung:	n/a	chr19:52772776-52772785 chr19:52773100-52773114 chr19:52773093-52773100 chr19:52773093-52773100 chr19:52773093-52773100
2	SP1	chr19:52772355-52773208	HCT-116	colon:	n/a	chr19:52772796-52772806 chr19:52772735-52772746 chr19:52772774-52772786 chr19:52772775-52772784 chr19:52772774-52772786
3	CEBPB	chr19:52772548-52773198	A549	lung:	n/a	chr19:52772693-52772710
4	POLR2A	chr19:52772457-52773698	MCF10A-Er-Src	breast:	n/a	n/a
5	ELF1	chr19:52772451-52773560	MCF-7	breast:	n/a	chr19:52772842-52772851 chr19:52772841-52772852 chr19:52772841-52772852
6	POLR2A	chr19:52772517-52773433	HUVEC	blood vessel:	n/a	n/a
7	MAX	chr19:52772498-52773456	NB4	blood:	n/a	n/a
8	CEBPB	chr19:52772464-52773135	HCT-116	colon:	n/a	chr19:52772693-52772710
9	RUNX3	chr19:52772468-52773650	GM12878	blood:	n/a	n/a
10	CEBPB	chr19:52772517-52773338	IMR90	lung:	n/a	chr19:52772693-52772710
11	USF1	chr19:52772538-52773189	A549	lung:	n/a	chr19:52772825-52772841
12	POLR2A	chr19:52772358-52773879	MCF-7	breast:	n/a	n/a
13	POLR2A	chr19:52772393-52773418	HepG2	liver:	n/a	n/a
14	CEBPB	chr19:52772519-52773202	MCF-7	breast:	n/a	chr19:52772693-52772710
15	POLR2A	chr19:52772437-52773350	U87	brain:	n/a	n/a
16	CEBPB	chr19:52772489-52773112	ECC-1	luminal epithelium:	n/a	chr19:52772693-52772710
17	SP1	chr19:52772439-52773221	A549	lung:	n/a	chr19:52772796-52772806 chr19:52772735-52772746 chr19:52772774-52772786 chr19:52772775-52772784 chr19:52772774-52772786
18	ETS1	chr19:52772786-52773088	A549	lung:	n/a	chr19:52772843-52772852 chr19:52772844-52772855 chr19:52772844-52772854 chr19:52772843-52772854 chr19:52772843-52772852
19	HEY1	chr19:52772491-52773337	HepG2	liver:	n/a	chr19:52773224-52773239
20	ELF1	chr19:52772585-52773350	K562	blood:	n/a	chr19:52772842-52772851 chr19:52772841-52772852 chr19:52772841-52772852
21	MAX	chr19:52772359-52773723	A549	lung:	n/a	n/a
22	POLR2A	chr19:52772492-52773884	Hela-S3	cervix:	n/a	n/a
23	MAX	chr19:52772544-52773256	K562	blood:	n/a	n/a
24	POU2F2	chr19:52772432-52773410	GM12878	blood:	n/a	chr19:52772495-52772516 chr19:52772500-52772511
25	CEBPB	chr19:52772602-52773112	HepG2	liver:	n/a	chr19:52772693-52772710
26	CREB1	chr19:52772474-52773299	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:52772454-52773872	GM18526	blood:	n/a	n/a
28	TAF1	chr19:52772577-52773206	GM12892	blood:	n/a	n/a
29	YY1	chr19:52772647-52773449	SK-N-SH	brain:	n/a	chr19:52773129-52773138 chr19:52773228-52773239
30	MAX	chr19:52772596-52773174	HepG2	liver:	n/a	n/a
31	MAZ	chr19:52772597-52773669	K562	blood:	n/a	n/a
32	GABPA	chr19:52772576-52773104	MCF-7	breast:	n/a	chr19:52772776-52772785
33	MAZ	chr19:52772452-52773315	GM12878	blood:	n/a	n/a
34	E2F6	chr19:52772602-52773297	K562	blood:	n/a	chr19:52772776-52772785 chr19:52773100-52773114 chr19:52773093-52773100 chr19:52773093-52773100 chr19:52773093-52773100
35	POLR2A	chr19:52772554-52773934	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:52772401-52773496	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr19:52772263-52774060	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr19:52772359-52773963	GM12892	blood:	n/a	n/a
39	MAX	chr19:52772456-52773450	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr19:52772469-52773427	K562	blood:	n/a	n/a
41	MAX	chr19:52772577-52773516	K562	blood:	n/a	n/a
42	TAF1	chr19:52772538-52773230	K562	blood:	n/a	n/a
43	POLR2A	chr19:52772359-52773509	K562	blood:	n/a	n/a
44	TAF1	chr19:52772524-52773227	GM12878	blood:	n/a	n/a
45	TAF1	chr19:52772432-52773186	PFSK-1	brain:	n/a	n/a
46	CREB1	chr19:52772588-52773115	H1-hESC	embryonic stem cell:	n/a	n/a
47	STAT1	chr19:52772607-52773192	GM12878	blood:	n/a	n/a
48	SIN3AK20	chr19:52772545-52773172	K562	blood:	n/a	n/a
49	POLR2A	chr19:52772444-52773546	GM12892	blood:	n/a	n/a
50	TCF7L2	chr19:52772733-52773175	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52773035-52773085	Jurkat	blood:	n/a
2	chr19:52773035-52773085	GM06990	blood:	n/a
3	chr19:52773035-52773085	IMR90	lung:	fetal
4	chr19:52773035-52773085	HPAEpiC	pulmonary alveolar:	n/a
5	chr19:52773035-52773085	U87	brain:	n/a
6	chr19:52773035-52773085	HL-60	blood:	n/a
7	chr19:52773035-52773085	HepG2	liver:	n/a
8	chr19:52773035-52773085	HCF	heart:	n/a
9	chr19:52773035-52773085	RPTEC	kidney:	n/a
10	chr19:52773035-52773085	Caco-2	colon:	n/a
11	chr19:52773035-52773085	NH-A	brain:	n/a
12	chr19:52773035-52773085	AG10803	skin:	n/a
13	chr19:52773035-52773085	HAEpiC	amniotic membrane:	n/a
14	chr19:52773035-52773085	PFSK-1	brain:	n/a
15	chr19:52773035-52773085	CMK	blood:	n/a
16	chr19:52773035-52773085	HCT-116	colon:	n/a
17	chr19:52773035-52773085	H1-hESC	embryonic stem cell:	embryo
18	chr19:52773035-52773085	ProgFib	skin:	n/a
19	chr19:52773035-52773085	HEK293	kidney:	embryo
20	chr19:52773035-52773085	AoSMC	blood vessel:	n/a
21	chr19:52773035-52773085	AG04450	lung:	fetal
22	chr19:52773035-52773085	SK-N-SH_RA	brain:	n/a
23	chr19:52773035-52773085	AG04449	skin:	fetal
24	chr19:52773035-52773085	NB4	blood:	n/a
25	chr19:52773035-52773085	SK-N-MC	brain:	n/a
26	chr19:52773035-52773085	SAEC	small airway:	n/a
27	chr19:52773035-52773085	SKMC	muscle:	n/a
28	chr19:52773035-52773085	MCF10A-Er-Src	breast:	n/a
29	chr19:52773035-52773085	A549	lung:	n/a
30	chr19:52773035-52773085	HMEC	breast:	n/a
31	chr19:52773035-52773085	HRPEpiC	eye:	n/a
32	chr19:52773035-52773085	GM12891	blood:	n/a
33	chr19:52773035-52773085	Hepatocyte	liver:	n/a
34	chr19:52773035-52773085	NT2-D1	testis:	n/a
35	chr19:52773035-52773085	HEEpiC	esophagus:	n/a
36	chr19:52773035-52773085	GM12878	blood:	n/a
37	chr19:52773035-52773085	HCM	heart:	n/a
38	chr19:52773035-52773085	ECC-1	luminal epithelium:	n/a
39	chr19:52773035-52773085	BE2_C	brain:	n/a
40	chr19:52773035-52773085	HRE	kidney:	n/a
41	chr19:52773035-52773085	HCPEpiC	choroid plexus:	n/a
42	chr19:52773035-52773085	T-47D	breast:	n/a
43	chr19:52773035-52773085	NHDF-neo	bronchial:	n/a
44	chr19:52773035-52773085	GM19239	blood:	n/a
45	chr19:52773035-52773085	PrEC	prostate:	n/a
46	chr19:52773035-52773085	HRCEpiC	kidney:	n/a
47	chr19:52773035-52773085	BJ	skin:	n/a
48	chr19:52773035-52773085	SK-N-SH	brain:	n/a
49	chr19:52773035-52773085	MCF-7	breast:	n/a
50	chr19:52773035-52773085	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52771242..52774496-chr19:52796154..52801198,5	MCF-7	breast:
2	chr19:52771473..52773658-chr19:52872286..52874915,2	MCF-7	breast:
3	chr19:52773000..52774618-chr19:52792454..52794386,2	K562	blood:
4	chr19:52771349..52773088-chr19:52900874..52902470,2	MCF-7	breast:
5	chr19:52772712..52774263-chr19:52799047..52800693,2	K562	blood:
6	chr19:52772026..52776261-chr19:52781637..52786393,5	K562	blood:
7	chr19:52771880..52774244-chr19:52838831..52841718,3	MCF-7	breast:
8	chr19:52772363..52775107-chr19:52799601..52802037,4	MCF-7	breast:
9	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:
10	chr19:52772873..52773677-chr2:32390867..32391602,2	Hela-S3	cervix:
11	chr19:52771362..52774263-chr19:52797982..52800693,2	K562	blood:
12	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:
13	chr19:52641013..52643402-chr19:52771783..52774070,3	MCF-7	breast:
14	chr19:52771196..52774040-chr19:52836837..52839956,3	MCF-7	breast:
15	chr19:52597459..52600188-chr19:52771516..52774031,2	MCF-7	breast:

Variant related genes	Relation type
ZNF766	TF binding region
ZNF766	CpG island
ENSG00000167554	Chromatin interaction
ENSG00000256087	Chromatin interaction
ENSG00000152683	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000198464	Chromatin interaction
ENSG00000221923	Chromatin interaction
ENSG00000208002	Chromatin interaction
ENSG00000167555	Chromatin interaction
ENSG00000197608	Chromatin interaction
ENSG00000269834	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000268015	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10426950	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2089275	0.81[AFR][1000 genomes]
rs2560871	0.81[AFR][1000 genomes]
rs2560873	0.81[AFR][1000 genomes]
rs2560875	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560877	0.82[AFR][1000 genomes]
rs2560904	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2560905	0.95[EUR][1000 genomes]
rs2657923	0.81[AFR][1000 genomes]
rs2657924	0.81[AFR][1000 genomes]
rs2657926	0.81[AFR][1000 genomes]
rs2657927	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2657930	0.85[AFR][1000 genomes]
rs62110405	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6509630	0.90[AFR][1000 genomes]
rs8112349	0.87[AFR][1000 genomes]
rs9304727	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52772200-52773400	Active TSS	Primary T cells from cord blood	blood
2	chr19:52772200-52773600	Active TSS	Brain Angular Gyrus	brain
3	chr19:52772200-52773600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:52772200-52773800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:52772200-52773800	Active TSS	Brain Germinal Matrix	brain
6	chr19:52772200-52773800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr19:52772200-52773800	Active TSS	Esophagus	oesophagus
8	chr19:52772200-52773800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr19:52772200-52774000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:52772200-52774000	Active TSS	Fetal Lung	lung
11	chr19:52772200-52774200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:52772200-52774200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:52772200-52774200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:52772200-52774200	Active TSS	A549	lung
15	chr19:52772400-52773400	Active TSS	Brain Substantia Nigra	brain
16	chr19:52772400-52773600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:52772400-52773600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr19:52772400-52773600	Active TSS	Hela-S3	cervix
19	chr19:52772400-52773600	Active TSS	HUVEC	blood vessel
20	chr19:52772400-52773800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr19:52772400-52773800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr19:52772400-52773800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:52772400-52773800	Active TSS	Colon Smooth Muscle	Colon
24	chr19:52772400-52773800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr19:52772400-52773800	Active TSS	Psoas Muscle	Psoas
26	chr19:52772400-52773800	Active TSS	Right Ventricle	heart
27	chr19:52772400-52773800	Active TSS	Thymus	Thymus
28	chr19:52772400-52773800	Active TSS	NHEK	skin
29	chr19:52772400-52774000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:52772400-52774000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:52772400-52774000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:52772400-52774000	Active TSS	Aorta	Aorta
33	chr19:52772400-52774000	Active TSS	Fetal Brain Male	brain
34	chr19:52772400-52774000	Active TSS	K562	blood
35	chr19:52772400-52774200	Active TSS	H9 Cell Line	embryonic stem cell
36	chr19:52772400-52774200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:52772400-52774200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr19:52772400-52774200	Active TSS	Fetal Intestine Large	intestine
39	chr19:52772400-52774200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr19:52772400-52774200	Active TSS	HSMMtube	muscle
41	chr19:52772400-52774200	Active TSS	NH-A	brain
42	chr19:52772400-52774400	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr19:52772400-52774400	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr19:52772400-52774400	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr19:52772400-52774400	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:52772400-52774400	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr19:52772400-52774400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:52772400-52774400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:52772400-52774400	Active TSS	HSMM	muscle
50	chr19:52772400-52774400	Active TSS	NHDF-Ad	bronchial

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