Variant report

Variant	rs12907952
Chromosome Location	chr15:52581150-52581151
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52514548..52516962-chr15:52580174..52582493,2	MCF-7	breast:
2	chr15:52580121..52581968-chr15:52819910..52822572,2	MCF-7	breast:
3	chr15:52532630..52535359-chr15:52579231..52581828,3	MCF-7	breast:
4	chr15:52580770..52583438-chr15:52859904..52862559,3	MCF-7	breast:
5	chr15:52580122..52582567-chr15:52617504..52619991,4	MCF-7	breast:
6	chr15:52579188..52581909-chr8:144948977..144951060,2	MCF-7	breast:
7	chr15:52580472..52581982-chr15:52945123..52947114,2	MCF-7	breast:
8	chr15:52579768..52582788-chr15:52819244..52821872,3	MCF-7	breast:
9	chr15:52580244..52584410-chr15:52619433..52625902,7	MCF-7	breast:
10	chr15:52580574..52582076-chr15:52967362..52969063,2	MCF-7	breast:
11	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:
12	chr15:50645603..50648552-chr15:52580814..52582749,4	MCF-7	breast:
13	chr15:52578087..52583541-chr15:52969803..52973267,6	MCF-7	breast:
14	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
15	chr15:52309835..52312480-chr15:52580964..52583747,3	MCF-7	breast:
16	chr15:52521470..52523349-chr15:52580283..52582342,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000197535	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000244879	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11854890	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12907067	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35982476	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4238390	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4442751	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4776034	0.82[EUR][1000 genomes]
rs55845575	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56071450	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57506065	0.91[EUR][1000 genomes]
rs62015972	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52554800-52582200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52555000-52585000	Weak transcription	Left Ventricle	heart
3	chr15:52556000-52587000	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:52565800-52587000	Weak transcription	Right Atrium	heart
5	chr15:52571200-52585800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:52571200-52587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:52574600-52587000	Weak transcription	Brain Anterior Caudate	brain
8	chr15:52575000-52585000	Weak transcription	Fetal Stomach	stomach
9	chr15:52575400-52582000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:52577400-52582000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:52579200-52581600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:52579200-52582200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:52579200-52582800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:52579400-52581400	Enhancers	Fetal Intestine Small	intestine
15	chr15:52579600-52583200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:52579800-52582000	Flanking Active TSS	HepG2	liver
17	chr15:52580000-52582200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr15:52580200-52581200	Flanking Active TSS	Hela-S3	cervix
19	chr15:52580200-52581600	Enhancers	Fetal Muscle Leg	muscle
20	chr15:52580200-52582400	Enhancers	Small Intestine	intestine
21	chr15:52580400-52581400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:52580400-52581400	Flanking Active TSS	Liver	Liver
23	chr15:52580400-52582200	Enhancers	Fetal Muscle Trunk	muscle
24	chr15:52580400-52582400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr15:52580400-52582400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:52580400-52582400	Enhancers	HSMMtube	muscle
27	chr15:52580400-52582600	Enhancers	Esophagus	oesophagus
28	chr15:52580400-52587000	Weak transcription	Right Ventricle	heart
29	chr15:52580600-52581200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr15:52580600-52581200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:52580600-52581200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:52580600-52581200	Enhancers	Adipose Nuclei	Adipose
33	chr15:52580600-52581200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr15:52580600-52581200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr15:52580600-52581200	Enhancers	Spleen	Spleen
36	chr15:52580600-52581400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr15:52580600-52581600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:52580600-52582200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:52580600-52582200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr15:52580600-52582400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr15:52580600-52582400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr15:52580600-52582400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:52580600-52582400	Enhancers	Gastric	stomach
44	chr15:52580800-52581200	Flanking Active TSS	Pancreas	Pancrea
45	chr15:52580800-52582400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:52580800-52582400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:52580800-52582400	Enhancers	Fetal Intestine Large	intestine
48	chr15:52580800-52582400	Enhancers	HMEC	breast
49	chr15:52580800-52582800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:52581000-52581400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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