Variant report

Variant	rs12906189
Chromosome Location	chr15:78444791-78444792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78442888..78445461-chr15:78457848..78460341,2	MCF-7	breast:
2	chr15:78437153..78440009-chr15:78444178..78446804,3	MCF-7	breast:
3	chr15:78441640..78443234-chr15:78443760..78445401,2	K562	blood:

Variant related genes	Relation type
ENSG00000166411	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11629561	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631100	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631653	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634325	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638547	1.00[ASN][1000 genomes]
rs12904404	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910386	1.00[ASN][1000 genomes]
rs12911405	1.00[ASN][1000 genomes]
rs12912695	0.84[ASN][1000 genomes]
rs12915634	1.00[ASN][1000 genomes]
rs2044098	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2868607	1.00[ASN][1000 genomes]
rs3087998	0.83[AMR][1000 genomes];0.87[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
rs12906189	IDH3A	cis	brain	BrainEAC

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78442600-78445200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:78442600-78447400	Weak transcription	Aorta	Aorta
3	chr15:78442600-78448000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:78442600-78451200	Weak transcription	Lung	lung
5	chr15:78442600-78451400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:78442600-78458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:78442800-78445400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:78442800-78445400	Weak transcription	HSMM	muscle
9	chr15:78442800-78445400	Weak transcription	HSMMtube	muscle
10	chr15:78442800-78447200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:78442800-78448000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:78442800-78448000	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:78442800-78448600	Weak transcription	Placenta	Placenta
14	chr15:78442800-78448800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:78442800-78449200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:78442800-78450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:78442800-78450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:78442800-78451800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:78442800-78451800	Weak transcription	Ovary	ovary
20	chr15:78442800-78452200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:78442800-78463400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:78442800-78465600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:78443000-78445400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:78443000-78445400	Weak transcription	Fetal Intestine Large	intestine
25	chr15:78443000-78445400	Weak transcription	Osteobl	bone
26	chr15:78443000-78446800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:78443000-78450000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:78443000-78450000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:78443000-78450200	Weak transcription	Fetal Stomach	stomach
30	chr15:78443000-78451600	Weak transcription	NH-A	brain
31	chr15:78443000-78452200	Weak transcription	HUVEC	blood vessel
32	chr15:78443200-78445600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:78443200-78447000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:78443200-78447200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:78443200-78447200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr15:78443200-78451200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:78443200-78451400	Weak transcription	Fetal Brain Female	brain
38	chr15:78443200-78451600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:78443200-78451800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:78443400-78445000	Weak transcription	Brain Angular Gyrus	brain
41	chr15:78443400-78445200	Weak transcription	Brain Anterior Caudate	brain
42	chr15:78443400-78445400	Weak transcription	Primary T cells from cord blood	blood
43	chr15:78443400-78445400	Weak transcription	Right Atrium	heart
44	chr15:78443400-78445400	Weak transcription	NHDF-Ad	bronchial
45	chr15:78443400-78446800	Weak transcription	Primary B cells from cord blood	blood
46	chr15:78443400-78447200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:78443400-78447400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:78443400-78447400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:78443400-78447400	Weak transcription	Fetal Lung	lung
50	chr15:78443400-78447400	Weak transcription	A549	lung

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