Variant report

Variant	rs28452388
Chromosome Location	chr15:78502086-78502087
allele	A/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	GATA3	chr15:78501509-78502753	MCF-7	breast:	n/a	chr15:78502120-78502133
2	TCF12	chr15:78501412-78502841	ECC-1	luminal epithelium:	n/a	n/a
3	GATA2	chr15:78501951-78502295	SH-SY5Y	brain:	n/a	chr15:78502120-78502133
4	REST	chr15:78501936-78502235	SK-N-SH	brain:	n/a	chr15:78502086-78502099 chr15:78502082-78502102 chr15:78502093-78502102
5	HA-E2F1	chr15:78501479-78502259	MCF-7	breast:	n/a	n/a
6	GATA3	chr15:78501599-78502785	MCF-7	breast:	n/a	chr15:78502120-78502133
7	MAX	chr15:78501545-78502088	ECC-1	luminal epithelium:	n/a	n/a
8	REST	chr15:78501945-78502295	ECC-1	luminal epithelium:	n/a	chr15:78502086-78502099 chr15:78502082-78502102 chr15:78502093-78502102
9	GATA3	chr15:78501778-78502565	MCF-7	breast:	n/a	chr15:78502120-78502133
10	REST	chr15:78501988-78502175	K562	blood:	n/a	chr15:78502086-78502099 chr15:78502082-78502102 chr15:78502093-78502102
11	POLR2A	chr15:78501729-78502146	ECC-1	luminal epithelium:	n/a	n/a
12	YY1	chr15:78501518-78502135	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr15:78501583-78502116	ECC-1	luminal epithelium:	n/a	n/a
14	GATA3	chr15:78501949-78502238	T-47D	breast:	n/a	chr15:78502120-78502133
15	REST	chr15:78501633-78502230	ECC-1	luminal epithelium:	n/a	chr15:78502086-78502099 chr15:78502082-78502102 chr15:78502093-78502102
16	NFIC	chr15:78501581-78502895	ECC-1	luminal epithelium:	n/a	n/a
17	ZNF217	chr15:78501701-78502797	MCF-7	breast:	n/a	n/a
18	POLR2A	chr15:78501649-78502220	ECC-1	luminal epithelium:	n/a	n/a
19	REST	chr15:78501925-78502198	Hela-S3	cervix:	n/a	chr15:78502086-78502099 chr15:78502082-78502102 chr15:78502093-78502102
20	EP300	chr15:78501479-78502896	ECC-1	luminal epithelium:	n/a	chr15:78502788-78502797 chr15:78501503-78501516
21	NFIC	chr15:78501517-78502954	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr15:78501547-78502173	MCF-7	breast:	n/a	n/a
23	GATA3	chr15:78502002-78502248	SH-SY5Y	brain:	n/a	chr15:78502120-78502133
24	TCF12	chr15:78501466-78502947	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78440397..78443186-chr15:78499689..78503898,3	MCF-7	breast:
2	chr15:78433373..78437251-chr15:78499302..78502813,3	MCF-7	breast:
3	chr15:78496538..78499859-chr15:78500154..78502705,3	MCF-7	breast:
4	chr15:78496325..78498387-chr15:78501053..78503232,2	MCF-7	breast:

Variant related genes	Relation type
ACSBG1	TF binding region
ENSG00000166411	Chromatin interaction
ENSG00000260988	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1011173	0.86[AMR][1000 genomes]
rs12441219	0.80[EUR][1000 genomes]
rs28722516	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57021464	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57491843	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58299587	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60968764	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62011377	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78493800-78504200	Enhancers	Brain Substantia Nigra	brain
2	chr15:78494200-78508800	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr15:78494200-78509800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr15:78494800-78508800	Enhancers	Brain Hippocampus Middle	brain
5	chr15:78494800-78509800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr15:78495000-78504200	Enhancers	Brain Cingulate Gyrus	brain
7	chr15:78495400-78502600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr15:78495400-78510000	Enhancers	Pancreas	Pancrea
9	chr15:78495400-78511000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr15:78496000-78507200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:78496400-78507800	Enhancers	Brain Anterior Caudate	brain
12	chr15:78496600-78502200	Weak transcription	K562	blood
13	chr15:78497200-78503800	Weak transcription	Lung	lung
14	chr15:78497200-78506800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr15:78498400-78503400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:78499200-78504000	Weak transcription	Right Ventricle	heart
17	chr15:78499600-78502200	Weak transcription	Fetal Heart	heart
18	chr15:78499600-78504400	Weak transcription	NHDF-Ad	bronchial
19	chr15:78499600-78504600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:78499600-78504800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:78499800-78502400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:78499800-78502400	Weak transcription	Osteobl	bone
23	chr15:78499800-78503600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:78500000-78502200	Weak transcription	HSMM	muscle
25	chr15:78500000-78504400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:78500200-78502200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:78500200-78502200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:78500800-78502600	Enhancers	Fetal Muscle Trunk	muscle
29	chr15:78500800-78506200	Enhancers	Brain Angular Gyrus	brain
30	chr15:78501200-78502600	Enhancers	Placenta	Placenta
31	chr15:78501200-78503400	Enhancers	Fetal Muscle Leg	muscle
32	chr15:78501200-78506200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:78501400-78502200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:78501400-78502600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:78501400-78502600	Enhancers	Esophagus	oesophagus
36	chr15:78501400-78502800	Enhancers	NHEK	skin
37	chr15:78501400-78503000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:78501400-78503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:78501400-78503400	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr15:78501400-78506000	Enhancers	Stomach Mucosa	stomach
41	chr15:78501600-78506000	Enhancers	Duodenum Mucosa	Duodenum
42	chr15:78501600-78506600	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr15:78501800-78502600	Enhancers	Adipose Nuclei	Adipose
44	chr15:78501800-78502600	Enhancers	Colonic Mucosa	Colon
45	chr15:78501800-78502600	Enhancers	Gastric	stomach
46	chr15:78501800-78502600	Enhancers	Left Ventricle	heart
47	chr15:78501800-78503000	Enhancers	Rectal Smooth Muscle	rectum
48	chr15:78501800-78503000	Enhancers	HSMMtube	muscle
49	chr15:78501800-78503200	Enhancers	Psoas Muscle	Psoas
50	chr15:78501800-78505800	Enhancers	Rectal Mucosa Donor 31	rectum

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