Variant report

Variant	rs542733
Chromosome Location	chr9:14098867-14098868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:14081509..14084690-chr9:14096320..14100204,3	MCF-7	breast:
2	chr9:14097652..14100494-chr9:14313670..14316038,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147862	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1743544	0.95[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs575660	0.95[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14075400-14116000	Weak transcription	Gastric	stomach
2	chr9:14078000-14112800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr9:14081400-14115800	Weak transcription	Hela-S3	cervix
4	chr9:14086000-14115600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:14090600-14115200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:14095400-14099000	Enhancers	HSMM	muscle
7	chr9:14095400-14099200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:14095800-14099200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:14096000-14099200	Active TSS	Aorta	Aorta
10	chr9:14096600-14099200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr9:14096600-14099200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr9:14096600-14099200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr9:14096600-14099400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr9:14096600-14099600	Weak transcription	Right Ventricle	heart
15	chr9:14096800-14099200	Enhancers	Fetal Brain Female	brain
16	chr9:14096800-14099200	Flanking Active TSS	A549	lung
17	chr9:14096800-14099400	Enhancers	Adipose Nuclei	Adipose
18	chr9:14096800-14099400	Enhancers	Colon Smooth Muscle	Colon
19	chr9:14096800-14099600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr9:14096800-14099800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:14096800-14120000	Weak transcription	Brain Substantia Nigra	brain
22	chr9:14097000-14099000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:14097400-14099000	Enhancers	Stomach Smooth Muscle	stomach
24	chr9:14097400-14099200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:14097400-14099200	Enhancers	NH-A	brain
26	chr9:14097400-14099200	Enhancers	Osteobl	bone
27	chr9:14097400-14103200	Weak transcription	Brain Angular Gyrus	brain
28	chr9:14097400-14111800	Weak transcription	Left Ventricle	heart
29	chr9:14097400-14135400	Weak transcription	HSMMtube	muscle
30	chr9:14097600-14099200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr9:14097600-14102400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:14097600-14102400	Weak transcription	Brain Germinal Matrix	brain
33	chr9:14097600-14112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:14097800-14099200	Enhancers	Brain Hippocampus Middle	brain
35	chr9:14097800-14107600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:14097800-14111800	Weak transcription	HMEC	breast
37	chr9:14098000-14099000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:14098200-14099200	Enhancers	Small Intestine	intestine
39	chr9:14098200-14100000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr9:14098200-14106600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:14098400-14099000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr9:14098400-14099000	Enhancers	Ovary	ovary
43	chr9:14098400-14099000	Enhancers	Stomach Mucosa	stomach
44	chr9:14098400-14099200	Enhancers	Liver	Liver
45	chr9:14098400-14099200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr9:14098400-14100200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr9:14098400-14102400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr9:14098400-14103000	Weak transcription	NHEK	skin
49	chr9:14098400-14115800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr9:14098600-14099000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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