Variant report

Variant	rs11854120
Chromosome Location	chr15:78448959-78448960
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr15:78448952-78449395	MCF10A-Er-Src	breast:	n/a	chr15:78449199-78449210 chr15:78449198-78449206 chr15:78449196-78449207

No.	Distal block	Cell Line	Cell type
1	chr15:78448588..78451426-chr15:78451804..78454242,3	MCF-7	breast:
2	chr15:78447133..78448969-chr15:78464297..78466316,2	K562	blood:
3	chr15:78440356..78444633-chr15:78445807..78449726,8	K562	blood:
4	chr15:78440797..78443276-chr15:78447048..78449109,3	MCF-7	breast:
5	chr15:78440387..78445053-chr15:78445574..78449184,7	K562	blood:

Variant related genes	Relation type
IDH3A	TF binding region
ENSG00000166411	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11856106	0.94[ASN][1000 genomes]
rs17479031	1.00[ASN][1000 genomes]
rs17479135	1.00[ASN][1000 genomes]
rs17850483	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17850484	1.00[ASN][1000 genomes]
rs3825847	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57867560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009331	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62009333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009336	1.00[EUR][1000 genomes]
rs62009337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009341	1.00[EUR][1000 genomes]
rs62009342	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009343	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009347	0.89[EUR][1000 genomes]
rs62009348	0.89[EUR][1000 genomes]
rs7165154	0.94[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

No data

Chromatin state (count:123 , 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	chr15:78442800-78449200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:78442800-78450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:78442800-78450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:78442800-78451800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:78442800-78451800	Weak transcription	Ovary	ovary
9	chr15:78442800-78452200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:78442800-78463400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:78442800-78465600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:78443000-78450000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:78443000-78450000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:78443000-78450200	Weak transcription	Fetal Stomach	stomach
15	chr15:78443000-78451600	Weak transcription	NH-A	brain
16	chr15:78443000-78452200	Weak transcription	HUVEC	blood vessel
17	chr15:78443200-78451200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:78443200-78451400	Weak transcription	Fetal Brain Female	brain
19	chr15:78443200-78451600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:78443200-78451800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:78443400-78449400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr15:78443400-78450200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:78443400-78452200	Weak transcription	Fetal Brain Male	brain
24	chr15:78443400-78452200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:78443400-78453400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:78443400-78454000	Weak transcription	Fetal Kidney	kidney
27	chr15:78443400-78458000	Weak transcription	Stomach Mucosa	stomach
28	chr15:78443600-78449000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:78443600-78450200	Weak transcription	Spleen	Spleen
30	chr15:78443600-78451400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:78443600-78451400	Weak transcription	Colonic Mucosa	Colon
32	chr15:78443600-78451800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:78443600-78451800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr15:78443600-78451800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:78443600-78452000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:78443600-78452200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:78443600-78452200	Weak transcription	Brain Substantia Nigra	brain
38	chr15:78443600-78452400	Weak transcription	Brain Germinal Matrix	brain
39	chr15:78443600-78453600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:78443600-78453600	Weak transcription	HepG2	liver
41	chr15:78443600-78453600	Weak transcription	K562	blood
42	chr15:78443600-78453600	Weak transcription	NHLF	lung
43	chr15:78443800-78450200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:78443800-78450200	Weak transcription	Pancreas	Pancrea
45	chr15:78443800-78452200	Weak transcription	Gastric	stomach
46	chr15:78444200-78453600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr15:78444400-78449600	Weak transcription	Small Intestine	intestine
48	chr15:78445400-78450200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr15:78445800-78451400	Weak transcription	Esophagus	oesophagus
50	chr15:78445800-78451600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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