Variant report

Variant	rs4278685
Chromosome Location	chr15:52550245-52550246
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:52549644-52550374	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr15:52549495-52550295	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr15:52549507-52550526	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr15:52549667-52550429	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr15:52549622-52550490	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr15:52549317-52550570	ECC-1	luminal epithelium:	n/a	chr15:52550268-52550284
7	TCF12	chr15:52549526-52550411	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr15:52549710-52550345	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr15:52549646-52550400	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr15:52549630-52550461	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr15:52549765-52550276	U87	brain:	n/a	n/a
12	SRF	chr15:52549636-52550348	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr15:52549678-52550273	ECC-1	luminal epithelium:	n/a	n/a
14	KAP1	chr15:52549683-52550254	HEK293	kidney:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
2	chr15:52549166..52552176-chr15:52598023..52601011,3	MCF-7	breast:
3	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:

No data

Variant related genes	Relation type
MYO5C	TF binding region
ENSG00000128833	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10851509	0.91[YRI][hapmap]
rs11070891	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4145157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4238389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4316698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4497629	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4776022	0.91[YRI][hapmap]
rs4776029	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4776032	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4776033	1.00[AMR][1000 genomes]
rs7169177	1.00[AMR][1000 genomes]
rs7171825	1.00[AMR][1000 genomes]
rs7172026	1.00[AMR][1000 genomes]
rs7175945	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs8030407	0.91[YRI][hapmap]
rs8043194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920688	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
2	chr15:52525800-52554000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:52536200-52553600	Weak transcription	Lung	lung
4	chr15:52536200-52553800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:52538000-52554600	Weak transcription	Colonic Mucosa	Colon
6	chr15:52539600-52553400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:52540000-52553800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:52542400-52553800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:52542800-52550400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:52542800-52550400	Enhancers	NH-A	brain
11	chr15:52543600-52555400	Weak transcription	Liver	Liver
12	chr15:52544400-52550600	Enhancers	NHDF-Ad	bronchial
13	chr15:52546800-52553600	Weak transcription	Spleen	Spleen
14	chr15:52546800-52553800	Weak transcription	Esophagus	oesophagus
15	chr15:52547000-52552000	Weak transcription	Gastric	stomach
16	chr15:52547000-52553400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:52547000-52555800	Weak transcription	Fetal Intestine Large	intestine
18	chr15:52547600-52553800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:52547800-52553400	Weak transcription	HMEC	breast
20	chr15:52548000-52550400	Enhancers	Fetal Heart	heart
21	chr15:52548200-52551000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:52548400-52550400	Enhancers	Fetal Thymus	thymus
23	chr15:52548400-52550600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:52548400-52551000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr15:52548600-52550400	Enhancers	Fetal Muscle Trunk	muscle
26	chr15:52548600-52550600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:52548600-52552000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:52548800-52550400	Enhancers	HSMMtube	muscle
29	chr15:52548800-52550600	Enhancers	Adipose Nuclei	Adipose
30	chr15:52548800-52550600	Enhancers	Osteobl	bone
31	chr15:52548800-52550800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:52548800-52551000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:52548800-52551200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr15:52548800-52551200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:52548800-52551400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr15:52549000-52550600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr15:52549000-52550800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr15:52549000-52551000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr15:52549000-52551400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr15:52549000-52553200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:52549000-52553400	Weak transcription	Primary B cells from cord blood	blood
42	chr15:52549000-52553800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:52549000-52557800	Weak transcription	Fetal Brain Male	brain
44	chr15:52549200-52550400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:52549200-52550600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr15:52549200-52550800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:52549200-52550800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:52549200-52550800	Enhancers	Fetal Muscle Leg	muscle
49	chr15:52549200-52552400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:52549200-52553600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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