Variant report

Variant	rs12907067
Chromosome Location	chr15:52587880-52587881
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	chr15:52587721-52588356	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:52587556-52588310	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr15:52586769-52588469	MCF-7	breast:	n/a	chr15:52587513-52587523
4	MYBL2	chr15:52587747-52588200	HepG2	liver:	n/a	n/a
5	FOXA2	chr15:52587692-52588256	A549	lung:	n/a	n/a
6	E2F6	chr15:52587739-52588263	A549	lung:	n/a	chr15:52588076-52588086
7	RCOR1	chr15:52587585-52588127	HepG2	liver:	n/a	n/a
8	YY1	chr15:52587767-52588189	SK-N-SH_RA	brain:	n/a	chr15:52587946-52587954 chr15:52588121-52588135 chr15:52587941-52587960 chr15:52588010-52588021
9	ZBTB7A	chr15:52587099-52588077	ECC-1	luminal epithelium:	n/a	chr15:52587456-52587465
10	HA-E2F1	chr15:52587035-52588474	MCF-7	breast:	n/a	chr15:52587072-52587079 chr15:52588076-52588086
11	MAX	chr15:52586952-52588376	HepG2	liver:	n/a	chr15:52587513-52587523
12	POLR2A	chr15:52587728-52588320	HCT-116	colon:	n/a	n/a
13	ELF1	chr15:52587877-52588218	HepG2	liver:	n/a	chr15:52588069-52588081 chr15:52587901-52587913
14	POLR2A	chr15:52587439-52588225	A549	lung:	n/a	n/a
15	NRF1	chr15:52587775-52588001	H1-hESC	embryonic stem cell:	n/a	chr15:52587886-52587900
16	MAX	chr15:52587696-52588211	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr15:52587854-52587936	HepG2	liver:	n/a	n/a
18	TBP	chr15:52587696-52588337	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAF1	chr15:52587623-52588193	A549	lung:	n/a	n/a
20	ZEB1	chr15:52587448-52588043	GM12878	blood:	n/a	chr15:52587719-52587728 chr15:52587710-52587719
21	ZEB1	chr15:52587576-52587968	GM12878	blood:	n/a	chr15:52587719-52587728 chr15:52587710-52587719
22	POLR2A	chr15:52587694-52588210	A549	lung:	n/a	n/a
23	TCF12	chr15:52587671-52588271	ECC-1	luminal epithelium:	n/a	n/a
24	PML	chr15:52587511-52588440	MCF-7	breast:	n/a	n/a
25	POLR2A	chr15:52587652-52588259	HCT-116	colon:	n/a	n/a
26	YY1	chr15:52587664-52588328	H1-hESC	embryonic stem cell:	n/a	chr15:52587946-52587954 chr15:52588121-52588135 chr15:52587941-52587960 chr15:52588010-52588021
27	TCF12	chr15:52587682-52588450	A549	lung:	n/a	n/a
28	POLR2A	chr15:52587513-52588389	ProgFib	skin:	n/a	n/a
29	E2F6	chr15:52587578-52588297	H1-hESC	embryonic stem cell:	n/a	chr15:52588076-52588086
30	GABPA	chr15:52587828-52588212	H1-hESC	embryonic stem cell:	n/a	chr15:52587886-52587900
31	POLR2A	chr15:52587872-52588063	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr15:52586997-52588259	H1-hESC	embryonic stem cell:	n/a	chr15:52587513-52587523
33	PAX5	chr15:52587870-52588132	GM12892	blood:	n/a	n/a
34	POLR2A	chr15:52587582-52588360	H1-hESC	embryonic stem cell:	n/a	n/a
35	NR2F2	chr15:52586942-52588424	MCF-7	breast:	n/a	n/a
36	CHD2	chr15:52587783-52588147	HepG2	liver:	n/a	n/a
37	TAF1	chr15:52587229-52588342	ECC-1	luminal epithelium:	n/a	n/a
38	E2F6	chr15:52587661-52588482	A549	lung:	n/a	chr15:52588076-52588086
39	YY1	chr15:52587592-52588343	ECC-1	luminal epithelium:	n/a	chr15:52587946-52587954 chr15:52588121-52588135 chr15:52587941-52587960 chr15:52588010-52588021
40	POLR2A	chr15:52587801-52588068	Hela-S3	cervix:	n/a	n/a
41	RFX5	chr15:52587879-52588187	HepG2	liver:	n/a	n/a
42	E2F6	chr15:52587725-52588359	H1-hESC	embryonic stem cell:	n/a	chr15:52588076-52588086
43	GATA3	chr15:52587758-52588111	T-47D	breast:	n/a	n/a
44	MAZ	chr15:52587798-52588193	HepG2	liver:	n/a	n/a
45	HDAC2	chr15:52586954-52588436	MCF-7	breast:	n/a	chr15:52587450-52587459
46	MAX	chr15:52587853-52588244	A549	lung:	n/a	n/a
47	BACH1	chr15:52587170-52588193	H1-hESC	embryonic stem cell:	n/a	n/a
48	CEBPD	chr15:52587779-52588220	HepG2	liver:	n/a	n/a
49	BHLHE40	chr15:52587746-52588089	HepG2	liver:	n/a	chr15:52587837-52587853 chr15:52587849-52587865 chr15:52588072-52588088
50	JUND	chr15:52587705-52588168	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52585776..52589284-chr15:52859101..52864638,8	MCF-7	breast:
2	chr15:52586746..52588342-chr15:52615809..52618694,2	MCF-7	breast:
3	chr15:52587606..52588238-chr16:56641774..56642685,2	HCT-116	colon:
4	chr15:52586831..52588797-chr15:52969729..52971575,2	MCF-7	breast:
5	chr15:52585351..52588570-chr15:52858851..52862304,3	MCF-7	breast:
6	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:
7	chr15:52586418..52589137-chr15:52642806..52644960,2	MCF-7	breast:
8	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
9	chr1:164755849..164758773-chr15:52587181..52589348,2	MCF-7	breast:
10	chr15:52584393..52589074-chr15:52819513..52822265,5	MCF-7	breast:

Variant related genes	Relation type
MYO5C	TF binding region
ENSG00000197535	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000125148	Chromatin interaction
ENSG00000185630	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11854890	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12907952	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35982476	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4238390	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4442751	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55845575	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56071450	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57506065	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62015972	0.84[AMR][1000 genomes];0.90[EUR][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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52586200-52588000	Active TSS	Pancreas	Pancrea
2	chr15:52586600-52588600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:52586800-52588200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr15:52586800-52588200	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr15:52586800-52588200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr15:52586800-52588400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr15:52586800-52588600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr15:52587000-52588000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:52587000-52588000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr15:52587000-52588000	Bivalent Enhancer	Fetal Brain Male	brain
11	chr15:52587000-52588200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:52587000-52588200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:52587000-52588200	Active TSS	Brain Anterior Caudate	brain
14	chr15:52587000-52588200	Active TSS	Duodenum Mucosa	Duodenum
15	chr15:52587000-52588200	Active TSS	Gastric	stomach
16	chr15:52587000-52588200	Bivalent/Poised TSS	NH-A	brain
17	chr15:52587000-52588400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr15:52587000-52588400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:52587000-52588400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr15:52587000-52588400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr15:52587000-52588400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr15:52587000-52588400	Active TSS	Hela-S3	cervix
23	chr15:52587000-52588600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr15:52587000-52588600	Enhancers	Fetal Heart	heart
25	chr15:52587200-52588000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:52587200-52588000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:52587200-52588000	Active TSS	Brain Cingulate Gyrus	brain
28	chr15:52587200-52588000	Flanking Bivalent TSS/Enh	Thymus	Thymus
29	chr15:52587200-52588200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:52587200-52588200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:52587200-52588200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
32	chr15:52587200-52588200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:52587200-52588200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:52587200-52588200	Bivalent/Poised TSS	Aorta	Aorta
35	chr15:52587200-52588200	Active TSS	Esophagus	oesophagus
36	chr15:52587200-52588200	Active TSS	Fetal Intestine Small	intestine
37	chr15:52587200-52588200	Flanking Active TSS	Psoas Muscle	Psoas
38	chr15:52587200-52588200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
39	chr15:52587200-52588200	Bivalent/Poised TSS	Osteobl	bone
40	chr15:52587200-52588400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr15:52587200-52588400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr15:52587200-52588400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr15:52587200-52588400	Active TSS	Brain Substantia Nigra	brain
44	chr15:52587200-52588400	Flanking Active TSS	HMEC	breast
45	chr15:52587400-52588000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:52587400-52588000	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr15:52587400-52588000	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
48	chr15:52587400-52588000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr15:52587400-52588000	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:52587400-52588000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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