Variant report

Variant	rs560339994
Chromosome Location	chr15:56034790-56034791
allele	C/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	HDAC2	chr15:56034672-56035202	MCF-7	breast:	n/a	n/a
2	REST	chr15:56034595-56034889	PFSK-1	brain:	n/a	chr15:56034747-56034756
3	POLR2A	chr15:56034304-56035650	Hela-S3	cervix:	n/a	n/a
4	HA-E2F1	chr15:56034537-56035563	Hela-S3	cervix:	n/a	chr15:56035370-56035380 chr15:56035020-56035034 chr15:56035354-56035364 chr15:56034720-56034735 chr15:56034690-56034699
5	POLR2A	chr15:56034368-56035590	HEK293	kidney:	n/a	n/a
6	CEBPB	chr15:56034423-56035080	Hela-S3	cervix:	n/a	n/a
7	TAF1	chr15:56034741-56035689	HepG2	liver:	n/a	n/a
8	SMARCB1	chr15:56033753-56036042	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr15:56033962-56035723	IMR90	lung:	n/a	chr15:56034632-56034641
10	MAZ	chr15:56034299-56035653	Hela-S3	cervix:	n/a	chr15:56034634-56034641 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
11	MAX	chr15:56034354-56034872	MCF-7	breast:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642
12	REST	chr15:56034542-56034984	PFSK-1	brain:	n/a	chr15:56034747-56034756
13	POLR2A	chr15:56033776-56035901	HepG2	liver:	n/a	n/a
14	TCF12	chr15:56034254-56035751	ECC-1	luminal epithelium:	n/a	chr15:56034864-56034871
15	MYC	chr15:56033992-56035562	A549	lung:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
16	MAX	chr15:56034286-56034901	MCF-7	breast:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642
17	TCF12	chr15:56034098-56036186	A549	lung:	n/a	chr15:56034864-56034871 chr15:56036136-56036146
18	REST	chr15:56034532-56035693	ECC-1	luminal epithelium:	n/a	chr15:56035363-56035376 chr15:56034747-56034756 chr15:56035619-56035628 chr15:56035386-56035395
19	MAX	chr15:56034405-56034833	K562	blood:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642
20	MAX	chr15:56034282-56035697	ECC-1	luminal epithelium:	n/a	chr15:56034634-56034641 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
21	MYC	chr15:56034395-56035540	MCF10A-Er-Src	breast:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
22	REST	chr15:56034676-56034889	SK-N-SH	brain:	n/a	chr15:56034747-56034756
23	RFX5	chr15:56034527-56034939	HepG2	liver:	n/a	n/a
24	POLR2A	chr15:56034590-56035781	A549	lung:	n/a	n/a
25	MAX	chr15:56034182-56035795	HepG2	liver:	n/a	chr15:56034634-56034641 chr15:56035766-56035776 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
26	POLR2A	chr15:56034315-56034804	Hela-S3	cervix:	n/a	n/a
27	REST	chr15:56034610-56034811	K562	blood:	n/a	chr15:56034747-56034756
28	FOXA2	chr15:56034252-56034954	A549	lung:	n/a	n/a
29	POLR2A	chr15:56034245-56035624	Hela-S3	cervix:	n/a	n/a
30	SIN3A	chr15:56033970-56035625	H1-hESC	embryonic stem cell:	n/a	chr15:56035360-56035371 chr15:56034906-56034919 chr15:56035334-56035345
31	MXI1	chr15:56032346-56036713	SK-N-SH	brain:	n/a	chr15:56034632-56034641
32	CHD2	chr15:56034289-56035750	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr15:56034760-56034910	GM12874	blood:	n/a	n/a
34	REST	chr15:56034391-56034869	PFSK-1	brain:	n/a	chr15:56034747-56034756
35	TBP	chr15:56034524-56034790	HepG2	liver:	n/a	n/a
36	MAX	chr15:56034424-56035492	H1-hESC	embryonic stem cell:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
37	POLR2A	chr15:56034779-56035712	H1-neurons	neurons:	n/a	n/a
38	TAF1	chr15:56034758-56035765	HepG2	liver:	n/a	n/a
39	MAX	chr15:56034198-56034811	SK-N-SH	brain:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642
40	ZKSCAN1	chr15:56034212-56034866	Hela-S3	cervix:	n/a	n/a
41	MAX	chr15:56034432-56034850	HepG2	liver:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642
42	TAF1	chr15:56034299-56034855	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr15:56033732-56035727	Hela-S3	cervix:	n/a	n/a
44	REST	chr15:56034664-56034853	GM12878	blood:	n/a	chr15:56034747-56034756
45	ZNF143	chr15:56034396-56034857	Hela-S3	cervix:	n/a	n/a
46	MAX	chr15:56034264-56035835	HepG2	liver:	n/a	chr15:56034634-56034641 chr15:56035766-56035776 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
47	MAX	chr15:56034320-56035691	ECC-1	luminal epithelium:	n/a	chr15:56034634-56034641 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
48	ZBTB7A	chr15:56034630-56036028	ECC-1	luminal epithelium:	n/a	chr15:56035663-56035671
49	MAX	chr15:56034363-56035598	A549	lung:	n/a	chr15:56034634-56034641 chr15:56035588-56035598 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642 chr15:56035366-56035376
50	MAX	chr15:56034342-56035054	SK-N-SH	brain:	n/a	chr15:56034634-56034641 chr15:56034633-56034642 chr15:56034631-56034639 chr15:56034632-56034642

No.	Distal block	Cell Line	Cell type
1	chr15:56033858..56036761-chr15:56051440..56053715,2	MCF-7	breast:
2	chr15:55965960..55968011-chr15:56032220..56035162,2	MCF-7	breast:
3	chr15:56033073..56035225-chr17:56708615..56710685,2	MCF-7	breast:
4	chr1:109645681..109648514-chr15:56034152..56035869,2	MCF-7	breast:
5	chr15:56034248..56036795-chr15:56038057..56039658,2	MCF-7	breast:
6	chr15:56031905..56035384-chr15:56036677..56038977,3	MCF-7	breast:

Variant related genes	Relation type
PRTG	TF binding region
ENSG00000259369	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000251484	Chromatin interaction
ENSG00000221218	Chromatin interaction
ENSG00000259369	Chromatin interaction
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv1052495	chr15:56013617-56102164	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3390617	chr15:56034285-56036833	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56031400-56036600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:56032600-56035400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:56032600-56036200	Active TSS	Fetal Kidney	kidney
4	chr15:56033000-56034800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:56033200-56036000	Active TSS	Placenta Amnion	Placenta Amnion
6	chr15:56033400-56036200	Active TSS	Ovary	ovary
7	chr15:56033600-56034800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
8	chr15:56033600-56034800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
9	chr15:56033600-56035000	Active TSS	Right Atrium	heart
10	chr15:56033600-56035600	Bivalent/Poised TSS	NHDF-Ad	bronchial
11	chr15:56033600-56035800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:56033600-56035800	Active TSS	Fetal Intestine Large	intestine
13	chr15:56033600-56035800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
14	chr15:56033600-56035800	Active TSS	Lung	lung
15	chr15:56033600-56036000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:56033600-56036000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
17	chr15:56033600-56036000	Active TSS	Aorta	Aorta
18	chr15:56033600-56036000	Active TSS	Right Ventricle	heart
19	chr15:56033600-56036200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
20	chr15:56033800-56034800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
21	chr15:56033800-56034800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
22	chr15:56033800-56034800	Active TSS	Psoas Muscle	Psoas
23	chr15:56033800-56035400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
24	chr15:56033800-56035600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
25	chr15:56033800-56035800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:56033800-56035800	Active TSS	Gastric	stomach
27	chr15:56034000-56035000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
28	chr15:56034000-56035600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:56034000-56035600	Active TSS	Placenta	Placenta
30	chr15:56034000-56035800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:56034000-56035800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:56034000-56035800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:56034000-56036000	Active TSS	A549	lung
34	chr15:56034000-56036200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr15:56034200-56034800	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
36	chr15:56034200-56035400	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr15:56034200-56035600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
38	chr15:56034200-56036000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:56034200-56036000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:56034200-56036000	Active TSS	Left Ventricle	heart
41	chr15:56034200-56036200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr15:56034200-56036200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
43	chr15:56034200-56036200	Active TSS	Fetal Lung	lung
44	chr15:56034400-56034800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr15:56034400-56035000	Bivalent/Poised TSS	Small Intestine	intestine
46	chr15:56034400-56035400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
47	chr15:56034400-56035400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:56034400-56035600	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:56034400-56035600	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:56034400-56035600	Flanking Bivalent TSS/Enh	HMEC	breast

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