Variant report

Variant	rs12339541
Chromosome Location	chr9:97638926-97638927
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97631226..97633221-chr9:97637766..97639575,2	MCF-7	breast:
2	chr9:97638818..97641619-chr9:97680155..97683255,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10217737	1.00[AFR][1000 genomes]
rs10512236	0.82[EUR][1000 genomes]
rs10993350	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10993374	1.00[AFR][1000 genomes]
rs10993381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993390	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10993391	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12337251	1.00[AFR][1000 genomes]
rs12342610	1.00[AFR][1000 genomes]
rs12344052	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349263	1.00[AFR][1000 genomes]
rs17356014	1.00[AFR][1000 genomes]
rs34032583	1.00[AFR][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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 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	chr9:97628600-97641000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:97630000-97645000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:97630200-97640800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr9:97630600-97643600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:97630800-97644200	Weak transcription	Adipose Nuclei	Adipose
6	chr9:97631000-97640000	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:97631800-97645600	Weak transcription	Small Intestine	intestine
8	chr9:97632000-97640600	Weak transcription	K562	blood
9	chr9:97632000-97646000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:97633400-97640600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr9:97633400-97646800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:97633400-97671800	Weak transcription	Esophagus	oesophagus
13	chr9:97634000-97646600	Weak transcription	Spleen	Spleen
14	chr9:97634000-97646800	Weak transcription	Stomach Mucosa	stomach
15	chr9:97634600-97640000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:97634800-97640000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:97635200-97640600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:97635200-97645600	Weak transcription	Placenta	Placenta
19	chr9:97635400-97644200	Weak transcription	Left Ventricle	heart
20	chr9:97635600-97642200	Weak transcription	Fetal Lung	lung
21	chr9:97635600-97644000	Weak transcription	Ovary	ovary
22	chr9:97636800-97641000	Weak transcription	Fetal Heart	heart
23	chr9:97637200-97640200	Weak transcription	NHEK	skin
24	chr9:97637200-97640800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:97637400-97640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:97637400-97640600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:97637400-97640800	Weak transcription	HMEC	breast
28	chr9:97637600-97639200	Enhancers	Brain Substantia Nigra	brain
29	chr9:97637600-97640200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:97637600-97641200	Weak transcription	NHLF	lung
31	chr9:97637800-97639200	Weak transcription	HepG2	liver
32	chr9:97637800-97640200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:97637800-97640800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:97637800-97643200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr9:97637800-97645200	Weak transcription	NH-A	brain
36	chr9:97638000-97640000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:97638000-97640000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:97638000-97640600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:97638000-97640600	Weak transcription	Psoas Muscle	Psoas
40	chr9:97638000-97640800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:97638200-97639800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr9:97638200-97640000	Weak transcription	HSMM	muscle
43	chr9:97638200-97640200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr9:97638200-97640600	Weak transcription	NHDF-Ad	bronchial
45	chr9:97638200-97640600	Weak transcription	Osteobl	bone
46	chr9:97638200-97644000	Weak transcription	Primary B cells from cord blood	blood
47	chr9:97638400-97639400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:97638400-97640000	Weak transcription	Brain Angular Gyrus	brain
49	chr9:97638400-97640000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:97638400-97640000	Weak transcription	Brain Inferior Temporal Lobe	brain

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