Variant report

Variant	rs12440659
Chromosome Location	chr15:40632302-40632303
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	POLR2A	chr15:40630789-40633526	U87	brain:	n/a	n/a
2	MAZ	chr15:40629940-40633888	IMR90	lung:	n/a	chr15:40632042-40632058
3	EP300	chr15:40632165-40633583	ECC-1	luminal epithelium:	n/a	chr15:40632913-40632929 chr15:40632926-40632942 chr15:40632245-40632252
4	POLR2A	chr15:40631842-40632622	ProgFib	skin:	n/a	n/a
5	NFIC	chr15:40632290-40633485	SK-N-SH	brain:	n/a	chr15:40633175-40633192
6	MXI1	chr15:40631720-40633980	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr15:40632197-40633568	ECC-1	luminal epithelium:	n/a	chr15:40633175-40633192
8	POLR2A	chr15:40630881-40633380	U87	brain:	n/a	n/a
9	TAF1	chr15:40632295-40633375	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr15:40630212-40633443	IMR90	lung:	n/a	n/a
11	POLR2A	chr15:40630776-40633457	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr15:40630896-40633380	U87	brain:	n/a	n/a
13	RAD21	chr15:40631041-40633804	SK-N-SH	brain:	n/a	chr15:40631917-40631929 chr15:40631915-40631928 chr15:40631917-40631927 chr15:40631912-40631931
14	TCF12	chr15:40632263-40633543	ECC-1	luminal epithelium:	n/a	chr15:40632682-40632689 chr15:40632912-40632922 chr15:40632778-40632788 chr15:40633250-40633257 chr15:40632922-40632932 chr15:40632518-40632526
15	POLR2A	chr15:40632001-40632639	PANC-1	pancreas:	n/a	n/a
16	ZBTB7A	chr15:40630110-40633237	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr15:40632229-40633426	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr15:40630215-40633532	U87	brain:	n/a	n/a
19	NFIC	chr15:40632268-40633555	ECC-1	luminal epithelium:	n/a	chr15:40633175-40633192
20	POLR2A	chr15:40630162-40633385	PANC-1	pancreas:	n/a	n/a
21	NFIC	chr15:40632205-40633640	SK-N-SH	brain:	n/a	chr15:40633175-40633192
22	TCF12	chr15:40632101-40633609	ECC-1	luminal epithelium:	n/a	chr15:40632682-40632689 chr15:40632912-40632922 chr15:40632778-40632788 chr15:40633250-40633257 chr15:40632922-40632932 chr15:40632518-40632526
23	ZBTB7A	chr15:40631716-40633480	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr15:40632155-40633420	SK-N-SH	brain:	n/a	n/a
25	RFX5	chr15:40632141-40632312	HepG2	liver:	n/a	n/a
26	POLR2A	chr15:40630896-40633272	HepG2	liver:	n/a	n/a
27	CTCF	chr15:40631286-40633790	SK-N-SH	brain:	n/a	chr15:40632784-40632793 chr15:40633471-40633484 chr15:40631914-40631927 chr15:40631916-40631926 chr15:40631912-40631928 chr15:40631913-40631934 chr15:40631911-40631929
28	CTCF	chr15:40632280-40632430	HVMF	connective:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40583247..40584804-chr15:40630582..40632469,2	MCF-7	breast:
2	chr15:40614221..40619136-chr15:40629898..40635011,9	K562	blood:
3	chr15:40581743..40583725-chr15:40632082..40634284,2	MCF-7	breast:
4	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
5	chr15:40631758..40634462-chr15:40659942..40662520,2	MCF-7	breast:
6	chr15:40628035..40631006-chr15:40631506..40634762,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf52-3	chr15:40632106-40632839	NONHSAT041829

Variant related genes	Relation type
C15orf52	TF binding region
ENSG00000140323	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000259368	Chromatin interaction
ENSG00000259330	Chromatin interaction
ENSG00000188549	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2004251	1.00[JPT][hapmap]
rs2118960	0.86[JPT][hapmap]
rs2412511	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs28405635	0.81[AMR][1000 genomes]
rs934935	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
2	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
3	chr15:40622400-40633800	Enhancers	Spleen	Spleen
4	chr15:40625800-40642800	Enhancers	Fetal Intestine Large	intestine
5	chr15:40626600-40633800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:40627000-40633400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:40628800-40633600	Enhancers	Placenta	Placenta
8	chr15:40629000-40632400	Enhancers	Fetal Intestine Small	intestine
9	chr15:40629400-40633600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:40629400-40637200	Enhancers	Fetal Lung	lung
11	chr15:40629600-40633400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:40629600-40633600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:40629600-40633600	Enhancers	Ovary	ovary
14	chr15:40629800-40632600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:40629800-40633600	Flanking Active TSS	Colonic Mucosa	Colon
16	chr15:40629800-40634000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr15:40630000-40632600	Flanking Active TSS	HSMMtube	muscle
18	chr15:40630000-40633400	Enhancers	Fetal Brain Male	brain
19	chr15:40630000-40633400	Flanking Active TSS	NH-A	brain
20	chr15:40630000-40633600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:40630000-40633600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr15:40630200-40632400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:40630200-40633000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr15:40630200-40633000	Flanking Active TSS	Osteobl	bone
25	chr15:40630200-40633200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:40630200-40633400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:40630400-40632400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:40630400-40632400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr15:40630400-40632600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:40630400-40632600	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr15:40630400-40632600	Flanking Active TSS	Hela-S3	cervix
32	chr15:40630400-40632800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:40630400-40633000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:40630400-40633400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr15:40630400-40633800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr15:40630400-40635400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr15:40630600-40632400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:40630600-40632400	Flanking Active TSS	A549	lung
39	chr15:40630600-40632400	Weak transcription	K562	blood
40	chr15:40630600-40632600	Enhancers	Liver	Liver
41	chr15:40630600-40632800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr15:40630600-40633000	Flanking Active TSS	NHDF-Ad	bronchial
43	chr15:40630600-40633200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr15:40630600-40636600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr15:40630800-40632800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:40630800-40633200	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr15:40631000-40632400	Enhancers	Fetal Brain Female	brain
48	chr15:40631000-40632400	Flanking Active TSS	Left Ventricle	heart
49	chr15:40631000-40633600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr15:40631200-40632600	Flanking Active TSS	Colon Smooth Muscle	Colon

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