Variant report

Variant	rs276924
Chromosome Location	chr18:28622524-28622525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28622482..28623001-chrX:152864333..152864870,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147382	Chromatin interaction
ENSG00000260081	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1790665	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2245035	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs276925	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs276927	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs276928	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs276929	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs276930	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs276931	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs276933	0.99[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	nsv833613	chr18:28446454-28623599	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv3388313	chr18:28583296-28693160	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv530788	chr18:28596461-28751891	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv961134	chr18:28612225-28625943	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28619400-28623200	Active TSS	Placenta Amnion	Placenta Amnion
2	chr18:28619800-28623200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:28620200-28623000	Active TSS	HMEC	breast
4	chr18:28620400-28623400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr18:28620600-28623000	Active TSS	NHEK	skin
6	chr18:28620600-28623800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr18:28620800-28623200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:28621000-28622600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
9	chr18:28621000-28622600	Bivalent Enhancer	Stomach Mucosa	stomach
10	chr18:28621000-28622800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr18:28621000-28622800	Bivalent/Poised TSS	Fetal Kidney	kidney
12	chr18:28621000-28623000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
13	chr18:28621000-28623000	Bivalent Enhancer	Liver	Liver
14	chr18:28621000-28623000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
15	chr18:28621000-28623000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr18:28621000-28623200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr18:28621000-28623200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr18:28621000-28623200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr18:28621000-28623400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr18:28621200-28622600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
21	chr18:28621200-28623000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr18:28621200-28623000	Bivalent/Poised TSS	Fetal Thymus	thymus
23	chr18:28621200-28623200	Active TSS	Esophagus	oesophagus
24	chr18:28621200-28623200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
25	chr18:28621400-28622600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr18:28621400-28622600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
27	chr18:28621400-28622600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
28	chr18:28621400-28622800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr18:28621400-28622800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
30	chr18:28621400-28622800	Bivalent Enhancer	Fetal Brain Male	brain
31	chr18:28621400-28623000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr18:28621400-28623000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr18:28621400-28623000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr18:28621400-28623000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
35	chr18:28621400-28623200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr18:28621400-28623200	Flanking Bivalent TSS/Enh	Right Ventricle	heart
37	chr18:28621400-28623200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
38	chr18:28621400-28623200	Bivalent/Poised TSS	Thymus	Thymus
39	chr18:28621400-28623600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
40	chr18:28621600-28623000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr18:28621600-28623000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr18:28621600-28623000	Bivalent Enhancer	Lung	lung
43	chr18:28621600-28623200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr18:28621600-28623200	Bivalent/Poised TSS	NH-A	brain
45	chr18:28621600-28623400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr18:28621800-28622600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr18:28621800-28622600	Bivalent Enhancer	Brain Angular Gyrus	brain
48	chr18:28621800-28623200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr18:28622000-28623000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr18:28622000-28623000	Bivalent/Poised TSS	Brain Anterior Caudate	brain

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