Variant report

Variant	rs56042870
Chromosome Location	chr15:74919778-74919779
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	POLR2A	chr15:74919456-74920284	H1-neurons	neurons:	n/a	n/a
2	MXI1	chr15:74919602-74919932	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:74919352-74921537	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:74918080-74923247	MCF-7	breast:	n/a	n/a
5	POLR2A	chr15:74906714-74928682	K562	blood:	n/a	n/a
6	SPI1	chr15:74919447-74919899	HL-60	blood:	n/a	chr15:74919665-74919674 chr15:74919663-74919676 chr15:74919657-74919670 chr15:74919664-74919677
7	EP300	chr15:74919777-74919847	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:74919769-74921969	NB4	blood:	n/a	n/a
9	SPI1	chr15:74919464-74919851	GM12891	blood:	n/a	chr15:74919665-74919674 chr15:74919663-74919676 chr15:74919657-74919670 chr15:74919664-74919677
10	POLR2A	chr15:74919393-74924631	HepG2	liver:	n/a	n/a
11	USF2	chr15:74919631-74919874	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:74915025-74921912	K562	blood:	n/a	n/a
13	SPI1	chr15:74919478-74919786	GM12878	blood:	n/a	chr15:74919665-74919674 chr15:74919663-74919676 chr15:74919657-74919670 chr15:74919664-74919677
14	POLR2A	chr15:74918554-74921653	GM12891	blood:	n/a	n/a
15	POLR2A	chr15:74917616-74925544	K562	blood:	n/a	n/a
16	POLR2A	chr15:74919742-74921260	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:74919659-74920349	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr15:74918698-74920307	PANC-1	pancreas:	n/a	n/a
19	MAZ	chr15:74919639-74919882	GM12878	blood:	n/a	n/a
20	EBF1	chr15:74919528-74919875	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:74918915-74921924	HL-60	blood:	n/a	n/a
22	POLR2A	chr15:74919389-74924155	GM12892	blood:	n/a	n/a
23	NFATC1	chr15:74919617-74920254	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:74919318-74921355	GM12891	blood:	n/a	n/a
25	POLR2A	chr15:74919658-74920920	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr15:74919470-74923707	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr15:74916327-74921769	A549	lung:	n/a	n/a
28	POLR2A	chr15:74919506-74920488	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr15:74918182-74920131	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:74915016-74925636	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:74919376-74921937	HepG2	liver:	n/a	n/a
32	POLR2A	chr15:74919446-74921266	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:74912457-74921873	HepG2	liver:	n/a	n/a
34	EBF1	chr15:74919513-74919882	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:74917569-74923850	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr15:74917322-74923933	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr15:74919417-74920312	U87	brain:	n/a	n/a
38	POLR2A	chr15:74919716-74920432	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr15:74914837-74924670	GM12878	blood:	n/a	n/a
40	POLR2A	chr15:74917345-74925986	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr15:74919478-74919795	SK-N-SH	brain:	n/a	n/a
42	SPI1	chr15:74919475-74919837	GM12891	blood:	n/a	chr15:74919665-74919674 chr15:74919663-74919676 chr15:74919657-74919670 chr15:74919664-74919677
43	POLR2A	chr15:74919400-74921221	GM12892	blood:	n/a	n/a
44	POLR2A	chr15:74919203-74923798	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr15:74919405-74921320	GM12891	blood:	n/a	n/a
46	MTA3	chr15:74919504-74920173	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:74919746-74921250	GM12878	blood:	n/a	n/a
48	POLR2A	chr15:74919736-74920327	HepG2	liver:	n/a	n/a
49	POLR2A	chr15:74919498-74919923	HepG2	liver:	n/a	n/a
50	POLR2A	chr15:74917728-74921937	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CLK3	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11547808	0.93[AFR][1000 genomes]
rs16968837	1.00[EUR][1000 genomes]
rs17861081	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17861082	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17861085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17861107	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17861108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17861121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28362893	1.00[EUR][1000 genomes]
rs28362919	1.00[EUR][1000 genomes]
rs34255805	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35570076	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35646069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36090160	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45527133	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4986880	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4986881	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4986882	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4986884	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57469673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58286051	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58573460	1.00[EUR][1000 genomes]
rs58763676	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59046618	1.00[EUR][1000 genomes]
rs59620060	1.00[EUR][1000 genomes]
rs59773112	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60032286	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60360792	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60439061	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60525627	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60814674	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61204492	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74025855	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1812223	chr15:74869438-74948063	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv1814078	chr15:74884447-74948063	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv457204	chr15:74885091-74948063	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv569991	chr15:74885091-74948063	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv542434	chr15:74885329-74929552	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1047943	chr15:74885329-74940857	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv817698	chr15:74889163-75019449	Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Flanking 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	54 gene(s)	inside rSNPs	diseases
11	esv19858	chr15:74911304-74925497	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv527730	chr15:74915888-74920532	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 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	chr15:74909000-74927000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:74910000-74931200	Strong transcription	NHLF	lung
3	chr15:74910000-74931600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:74910400-74925600	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr15:74910400-74931800	Strong transcription	K562	blood
6	chr15:74910400-74933400	Strong transcription	Rectal Smooth Muscle	rectum
7	chr15:74910600-74936400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:74910800-74922600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:74910800-74933200	Strong transcription	Fetal Intestine Large	intestine
10	chr15:74910800-74933800	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:74910800-74934400	Strong transcription	Thymus	Thymus
12	chr15:74911000-74927600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:74911000-74934200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:74911000-74934200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:74911000-74938000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:74911200-74926400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:74911400-74929600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:74911400-74929800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:74911400-74934800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:74911400-74936800	Strong transcription	Dnd41	blood
21	chr15:74911400-74937400	Strong transcription	Primary T cells from cord blood	blood
22	chr15:74911600-74920400	Strong transcription	Osteobl	bone
23	chr15:74911600-74921200	Strong transcription	Fetal Kidney	kidney
24	chr15:74911600-74921600	Strong transcription	HSMM	muscle
25	chr15:74911600-74921800	Strong transcription	HUVEC	blood vessel
26	chr15:74911600-74922600	Strong transcription	NHDF-Ad	bronchial
27	chr15:74911600-74925400	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr15:74911600-74926400	Strong transcription	Aorta	Aorta
29	chr15:74911600-74927400	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr15:74911600-74928200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:74911600-74928200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:74911600-74933000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:74911600-74933800	Strong transcription	Fetal Lung	lung
34	chr15:74911800-74923200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:74911800-74933200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:74911800-74934200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:74912000-74921800	Strong transcription	NH-A	brain
38	chr15:74912400-74921400	Strong transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:74913600-74919800	Strong transcription	Placenta	Placenta
40	chr15:74913600-74921200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr15:74913600-74921800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:74913600-74923000	Strong transcription	HepG2	liver
43	chr15:74913600-74927200	Weak transcription	Fetal Heart	heart
44	chr15:74913600-74932800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:74913600-74933000	Strong transcription	Colon Smooth Muscle	Colon
46	chr15:74913600-74934400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:74913800-74921600	Strong transcription	A549	lung
48	chr15:74913800-74922600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr15:74913800-74923800	Strong transcription	Fetal Muscle Leg	muscle
50	chr15:74913800-74933200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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