Variant report

Variant	rs10425164
Chromosome Location	chr19:19573196-19573197
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	ZNF143	chr19:19573103-19573292	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP4	chr19:19572811-19573406	H1-hESC	embryonic stem cell:	n/a	chr19:19573202-19573218
3	SIN3A	chr19:19572498-19573568	H1-hESC	embryonic stem cell:	n/a	chr19:19572550-19572559 chr19:19573310-19573319
4	TCF12	chr19:19573084-19573408	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr19:19572820-19573563	ECC-1	luminal epithelium:	n/a	n/a
6	MAFK	chr19:19573131-19573305	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:19573093-19573546	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr19:19572945-19573772	K562	blood:	n/a	n/a
9	RAD21	chr19:19573101-19573311	H1-hESC	embryonic stem cell:	n/a	chr19:19573270-19573283 chr19:19573126-19573140 chr19:19573182-19573192
10	MAX	chr19:19572859-19573473	H1-hESC	embryonic stem cell:	n/a	n/a
11	MXI1	chr19:19572680-19573744	SK-N-SH	brain:	n/a	n/a
12	MXI1	chr19:19573085-19573609	H1-hESC	embryonic stem cell:	n/a	n/a
13	ATF2	chr19:19572843-19573328	H1-hESC	embryonic stem cell:	n/a	n/a
14	BACH1	chr19:19573105-19573299	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3AK20	chr19:19573121-19573361	K562	blood:	n/a	n/a
16	POLR2A	chr19:19572698-19573497	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr19:19572717-19573371	H1-hESC	embryonic stem cell:	n/a	n/a
18	NFIC	chr19:19572912-19573735	ECC-1	luminal epithelium:	n/a	chr19:19573348-19573365 chr19:19573348-19573364
19	KAP1	chr19:19572481-19573519	HEK293	kidney:	n/a	n/a
20	EP300	chr19:19572964-19573442	H1-hESC	embryonic stem cell:	n/a	chr19:19573083-19573099 chr19:19573189-19573205
21	YY1	chr19:19573132-19573334	K562	blood:	n/a	chr19:19573243-19573254
22	MAX	chr19:19572624-19573470	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZBTB7A	chr19:19573100-19573295	K562	blood:	n/a	n/a
24	TAF1	chr19:19572836-19573478	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr19:19572939-19573225	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAZ	chr19:19572985-19573360	K562	blood:	n/a	n/a
27	GTF2F1	chr19:19573174-19573328	H1-hESC	embryonic stem cell:	n/a	n/a
28	CHD2	chr19:19573050-19573388	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr19:19573112-19573322	H1-hESC	embryonic stem cell:	n/a	chr19:19573264-19573273
30	NFIC	chr19:19572860-19573710	ECC-1	luminal epithelium:	n/a	chr19:19573348-19573365 chr19:19573348-19573364
31	SP1	chr19:19572935-19573341	H1-hESC	embryonic stem cell:	n/a	chr19:19573243-19573252 chr19:19573205-19573219 chr19:19573239-19573253 chr19:19573206-19573215 chr19:19573205-19573214 chr19:19573262-19573271 chr19:19573243-19573253 chr19:19573262-19573271 chr19:19573204-19573216 chr19:19573261-19573273 chr19:19573204-19573216 chr19:19573205-19573215 chr19:19573263-19573272 chr19:19573242-19573254 chr19:19573261-19573273 chr19:19573205-19573215 chr19:19573242-19573254
32	SP1	chr19:19572786-19573496	H1-hESC	embryonic stem cell:	n/a	chr19:19573243-19573252 chr19:19573205-19573219 chr19:19573239-19573253 chr19:19573206-19573215 chr19:19573205-19573214 chr19:19573262-19573271 chr19:19573243-19573253 chr19:19573262-19573271 chr19:19573204-19573216 chr19:19573261-19573273 chr19:19573204-19573216 chr19:19573205-19573215 chr19:19573263-19573272 chr19:19573242-19573254 chr19:19573261-19573273 chr19:19573205-19573215 chr19:19573242-19573254
33	POLR2A	chr19:19573196-19573392	K562	blood:	n/a	n/a
34	TCF12	chr19:19572857-19573546	ECC-1	luminal epithelium:	n/a	n/a
35	ZNF263	chr19:19571278-19573525	HEK293-T-REx	kidney:	n/a	chr19:19572602-19572623 chr19:19572607-19572616 chr19:19573057-19573066
36	JUND	chr19:19572736-19573312	H1-hESC	embryonic stem cell:	n/a	chr19:19573264-19573273
37	POLR2A	chr19:19573060-19573428	HUVEC	blood vessel:	n/a	n/a
38	KAP1	chr19:19572903-19573443	U2OS	brain:	n/a	n/a
39	CREB1	chr19:19572934-19573473	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr19:19572583-19574335	H1-hESC	embryonic stem cell:	n/a	n/a
41	TCF12	chr19:19573067-19573378	H1-hESC	embryonic stem cell:	n/a	n/a
42	REST	chr19:19573055-19573499	SK-N-SH	brain:	n/a	n/a
43	TCF12	chr19:19572831-19573526	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr19:19572767-19573487	H1-hESC	embryonic stem cell:	n/a	n/a
45	GABPA	chr19:19573020-19573388	H1-hESC	embryonic stem cell:	n/a	n/a
46	CHD2	chr19:19573179-19573241	K562	blood:	n/a	n/a
47	SIN3AK20	chr19:19573045-19573390	H1-hESC	embryonic stem cell:	n/a	n/a
48	FOXP2	chr19:19572932-19573438	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19526712..19528418-chr19:19572196..19573784,2	MCF-7	breast:
2	chr19:19515386..19519519-chr19:19571187..19573375,3	K562	blood:
3	chr19:19571238..19573571-chr19:19586807..19589450,2	MCF-7	breast:
4	chr19:19570376..19575066-chr19:19577857..19582377,6	K562	blood:
5	chr19:19571714..19574433-chr19:19574654..19576215,2	K562	blood:
6	chr19:19569495..19572698-chr19:19572718..19574339,3	K562	blood:

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10401822	1.00[AMR][1000 genomes]
rs10403737	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405475	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412351	0.89[AFR][1000 genomes]
rs10413582	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416335	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10421166	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423535	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425574	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13344439	0.89[AMR][1000 genomes]
rs16996102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55927831	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59344441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60455087	0.89[AMR][1000 genomes]
rs73922887	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922890	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922895	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922896	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9304961	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19567000-19573600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr19:19567000-19575000	Enhancers	Spleen	Spleen
3	chr19:19567000-19576200	Enhancers	Gastric	stomach
4	chr19:19567000-19576600	Genic enhancers	Fetal Intestine Small	intestine
5	chr19:19567200-19576000	Enhancers	Fetal Intestine Large	intestine
6	chr19:19567400-19575000	Enhancers	Small Intestine	intestine
7	chr19:19568200-19575600	Enhancers	Lung	lung
8	chr19:19568200-19575800	Enhancers	Placenta	Placenta
9	chr19:19568400-19575400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr19:19568600-19575400	Enhancers	Liver	Liver
11	chr19:19568600-19575400	Enhancers	Psoas Muscle	Psoas
12	chr19:19568600-19575600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:19568600-19575800	Enhancers	Left Ventricle	heart
14	chr19:19568600-19575800	Enhancers	Right Atrium	heart
15	chr19:19568600-19576000	Enhancers	Fetal Lung	lung
16	chr19:19568600-19576200	Enhancers	Stomach Mucosa	stomach
17	chr19:19568600-19576400	Enhancers	Pancreas	Pancrea
18	chr19:19568800-19574800	Enhancers	HSMMtube	muscle
19	chr19:19568800-19575000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr19:19568800-19575000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr19:19569000-19575400	Enhancers	Right Ventricle	heart
22	chr19:19569000-19575800	Enhancers	Esophagus	oesophagus
23	chr19:19569200-19575600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:19569200-19575800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:19569200-19576200	Weak transcription	Hela-S3	cervix
26	chr19:19569400-19573800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr19:19569400-19575800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:19569600-19573200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:19569600-19575400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr19:19569600-19575600	Enhancers	Brain Substantia Nigra	brain
31	chr19:19569800-19573400	Enhancers	K562	blood
32	chr19:19569800-19573800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:19569800-19575600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr19:19570200-19573200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr19:19570200-19574800	Enhancers	Fetal Heart	heart
36	chr19:19570200-19575000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:19570200-19575600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr19:19570400-19573600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr19:19570400-19574600	Enhancers	Brain Angular Gyrus	brain
40	chr19:19570400-19575000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr19:19570400-19575400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr19:19570400-19575600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:19570400-19575800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:19570400-19575800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr19:19570400-19575800	Enhancers	HMEC	breast
46	chr19:19570400-19576000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:19570600-19575600	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr19:19570600-19575800	Enhancers	Brain Cingulate Gyrus	brain
49	chr19:19570800-19573600	Flanking Active TSS	Fetal Thymus	thymus
50	chr19:19570800-19574400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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