Variant report

Variant	rs73564225
Chromosome Location	chr19:45667723-45667724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr19:45667623-45668207	GM12878	blood:	n/a	chr19:45668040-45668049
2	POLR2A	chr19:45667571-45668389	GM12878	blood:	n/a	n/a
3	STAT5A	chr19:45667451-45668265	GM12878	blood:	n/a	n/a
4	RUNX3	chr19:45667434-45668355	GM12878	blood:	n/a	n/a
5	RUNX3	chr19:45667573-45668292	GM12878	blood:	n/a	n/a
6	WRNIP1	chr19:45667522-45667992	GM12878	blood:	n/a	n/a
7	ELF1	chr19:45667067-45668678	GM12878	blood:	n/a	n/a
8	NFIC	chr19:45667489-45667931	GM12878	blood:	n/a	n/a
9	CHD2	chr19:45667704-45668246	GM12878	blood:	n/a	n/a
10	RELA	chr19:45667672-45668274	GM18951	blood:	n/a	n/a
11	POLR2A	chr19:45667591-45667845	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:45667640-45668296	GM12878	blood:	n/a	n/a
13	MTA3	chr19:45667710-45668017	GM12878	blood:	n/a	n/a
14	RELA	chr19:45667646-45668248	GM10847	blood:	n/a	n/a
15	PML	chr19:45667398-45668470	GM12878	blood:	n/a	n/a
16	MXI1	chr19:45667690-45668251	GM12878	blood:	n/a	n/a
17	ELF1	chr19:45667585-45668133	GM12878	blood:	n/a	n/a
18	RCOR1	chr19:45667634-45668217	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:45667693-45668212	GM12892	blood:	n/a	n/a
20	SP1	chr19:45667659-45668239	GM12878	blood:	n/a	n/a
21	CTCF	chr19:45667580-45667730	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:45666954-45668313	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:45667598-45667791	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:45667561-45668407	A549	lung:	n/a	n/a
25	RELA	chr19:45667672-45668254	GM19099	blood:	n/a	n/a
26	MTA3	chr19:45667147-45668640	GM12878	blood:	n/a	n/a
27	EBF1	chr19:45667426-45668392	GM12878	blood:	n/a	n/a
28	TCF12	chr19:45667633-45668419	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr19:45667642-45668312	GM19099	blood:	n/a	n/a
30	POLR2A	chr19:45667614-45667751	ProgFib	skin:	n/a	n/a
31	POLR2A	chr19:45667548-45668260	GM12878	blood:	n/a	n/a
32	RELA	chr19:45667518-45668306	GM12891	blood:	n/a	n/a
33	EBF1	chr19:45667333-45668274	GM12878	blood:	n/a	n/a
34	EBF1	chr19:45667679-45668190	GM12878	blood:	n/a	n/a
35	CTCF	chr19:45667680-45667830	GM12872	blood:	n/a	n/a
36	BCL3	chr19:45667219-45668376	A549	lung:	n/a	chr19:45667604-45667613 chr19:45668040-45668049
37	POLR2A	chr19:45667672-45668520	HL-60	blood:	n/a	n/a
38	POLR2A	chr19:45667436-45668254	GM12891	blood:	n/a	n/a
39	PAX5	chr19:45667593-45668288	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:45667616-45668365	GM12892	blood:	n/a	n/a
41	POU2F2	chr19:45667650-45668163	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45646729..45650244-chr19:45666195..45669472,3	MCF-7	breast:
2	chr19:45664293..45670548-chr19:45677917..45684715,10	MCF-7	breast:
3	chr19:45663965..45672033-chr19:45672145..45675901,9	K562	blood:
4	chr19:45579089..45581981-chr19:45667540..45670366,2	K562	blood:
5	chr19:45667124..45670268-chr19:45680467..45683235,3	K562	blood:
6	chr19:45664074..45668689-chr19:45680998..45684242,7	MCF-7	breast:
7	chr19:45558584..45560889-chr19:45665988..45668898,2	K562	blood:
8	chr19:45665641..45668911-chr19:45670300..45671967,3	K562	blood:
9	chr19:45665456..45669944-chr19:45672662..45676859,4	MCF-7	breast:
10	chr19:45662322..45668242-chr19:45680645..45684470,7	K562	blood:

No data

Variant related genes	Relation type
NKPD1	TF binding region
ENSG00000267545	Chromatin interaction
ENSG00000170684	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000189114	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1048552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12459817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12460178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12461733	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12463298	0.83[AMR][1000 genomes]
rs12463327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57302271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57627123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58504789	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59215448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60460304	1.00[AMR][1000 genomes]
rs6509200	0.85[AFR][1000 genomes]
rs73564216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564218	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	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

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45657800-45668200	Weak transcription	Right Atrium	heart
2	chr19:45660200-45674000	Weak transcription	A549	lung
3	chr19:45662800-45669000	Enhancers	Esophagus	oesophagus
4	chr19:45664000-45670200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:45664200-45667800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:45664200-45668400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:45665400-45669800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:45665400-45670000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:45665400-45670200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:45665400-45680400	Weak transcription	Brain Substantia Nigra	brain
11	chr19:45665400-45680600	Weak transcription	Fetal Lung	lung
12	chr19:45665600-45667800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:45665600-45680400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:45665800-45674600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:45665800-45680200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:45665800-45680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:45666000-45668000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:45666000-45669200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr19:45666000-45669200	Enhancers	HMEC	breast
20	chr19:45666000-45669800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:45666200-45668800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr19:45666400-45667800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:45666400-45668600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr19:45666400-45670400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr19:45666600-45668400	Enhancers	NHEK	skin
26	chr19:45666600-45669000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr19:45666600-45671000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr19:45666800-45667800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:45666800-45668000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr19:45666800-45668800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr19:45667000-45668000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr19:45667000-45668600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr19:45667000-45669000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:45667000-45669000	Enhancers	Right Ventricle	heart
35	chr19:45667000-45669200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:45667000-45669200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:45667000-45670400	Enhancers	Fetal Thymus	thymus
38	chr19:45667000-45670600	Enhancers	Placenta	Placenta
39	chr19:45667200-45668200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:45667200-45668200	Flanking Active TSS	HepG2	liver
41	chr19:45667200-45668400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr19:45667200-45668400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr19:45667200-45668400	Enhancers	Stomach Mucosa	stomach
44	chr19:45667200-45668600	Enhancers	Primary T cells from cord blood	blood
45	chr19:45667200-45668600	Enhancers	Duodenum Mucosa	Duodenum
46	chr19:45667200-45668800	Enhancers	Primary hematopoietic stem cells	blood
47	chr19:45667200-45668800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:45667200-45668800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:45667200-45669200	Enhancers	Primary B cells from peripheral blood	blood
50	chr19:45667400-45667800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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