Variant report

Variant	rs12438666
Chromosome Location	chr15:78450170-78450171
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	chr15:78448588..78451426-chr15:78451804..78454242,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166411	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11638921	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12904700	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1982241	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304825	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816253	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495276	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12438666	IDH3A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78442600-78451200	Weak transcription	Lung	lung
2	chr15:78442600-78451400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:78442600-78458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:78442800-78450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:78442800-78451800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:78442800-78451800	Weak transcription	Ovary	ovary
7	chr15:78442800-78452200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:78442800-78463400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:78442800-78465600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:78443000-78450200	Weak transcription	Fetal Stomach	stomach
11	chr15:78443000-78451600	Weak transcription	NH-A	brain
12	chr15:78443000-78452200	Weak transcription	HUVEC	blood vessel
13	chr15:78443200-78451200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:78443200-78451400	Weak transcription	Fetal Brain Female	brain
15	chr15:78443200-78451600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:78443200-78451800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:78443400-78450200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:78443400-78452200	Weak transcription	Fetal Brain Male	brain
19	chr15:78443400-78452200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:78443400-78453400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:78443400-78454000	Weak transcription	Fetal Kidney	kidney
22	chr15:78443400-78458000	Weak transcription	Stomach Mucosa	stomach
23	chr15:78443600-78450200	Weak transcription	Spleen	Spleen
24	chr15:78443600-78451400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:78443600-78451400	Weak transcription	Colonic Mucosa	Colon
26	chr15:78443600-78451800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:78443600-78451800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:78443600-78451800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:78443600-78452000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:78443600-78452200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:78443600-78452200	Weak transcription	Brain Substantia Nigra	brain
32	chr15:78443600-78452400	Weak transcription	Brain Germinal Matrix	brain
33	chr15:78443600-78453600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:78443600-78453600	Weak transcription	HepG2	liver
35	chr15:78443600-78453600	Weak transcription	K562	blood
36	chr15:78443600-78453600	Weak transcription	NHLF	lung
37	chr15:78443800-78450200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:78443800-78450200	Weak transcription	Pancreas	Pancrea
39	chr15:78443800-78452200	Weak transcription	Gastric	stomach
40	chr15:78444200-78453600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:78445400-78450200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:78445800-78451400	Weak transcription	Esophagus	oesophagus
43	chr15:78445800-78451600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:78445800-78451600	Weak transcription	NHDF-Ad	bronchial
45	chr15:78445800-78453600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:78445800-78464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:78446600-78450600	Strong transcription	Primary T cells from cord blood	blood
48	chr15:78446600-78465200	Strong transcription	Fetal Intestine Large	intestine
49	chr15:78446800-78466000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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