Variant report

Variant	rs56086075
Chromosome Location	chr10:28286823-28286824
allele	A/T
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	TCF7L2	chr10:28286692-28287050	HEK293	kidney:	n/a	chr10:28286809-28286816 chr10:28286809-28286818
2	FOXA1	chr10:28286641-28287027	HepG2	liver:	n/a	chr10:28286860-28286875 chr10:28286878-28286893
3	FOXA2	chr10:28286749-28287016	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000233472	TF binding region
ARMC4	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11006838	1.00[EUR][1000 genomes]
rs11814132	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11818080	1.00[EUR][1000 genomes]
rs11818106	1.00[EUR][1000 genomes]
rs16927673	1.00[EUR][1000 genomes]
rs2225713	1.00[EUR][1000 genomes]
rs28398887	1.00[EUR][1000 genomes]
rs28776270	1.00[EUR][1000 genomes]
rs56335062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56352562	1.00[EUR][1000 genomes]
rs57130444	1.00[EUR][1000 genomes]
rs57643587	1.00[EUR][1000 genomes]
rs58628171	1.00[EUR][1000 genomes]
rs58720058	1.00[EUR][1000 genomes]
rs59051253	1.00[EUR][1000 genomes]
rs59271137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59540473	1.00[EUR][1000 genomes]
rs59741264	1.00[EUR][1000 genomes]
rs60814150	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61344519	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61345755	1.00[EUR][1000 genomes]
rs61476792	1.00[EUR][1000 genomes]
rs61610224	1.00[EUR][1000 genomes]
rs7071799	1.00[EUR][1000 genomes]
rs7072445	1.00[EUR][1000 genomes]
rs7074114	1.00[EUR][1000 genomes]
rs7078174	1.00[EUR][1000 genomes]
rs7078969	1.00[EUR][1000 genomes]
rs7081199	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7093804	1.00[EUR][1000 genomes]
rs7097374	1.00[EUR][1000 genomes]
rs7100534	1.00[EUR][1000 genomes]
rs7100957	1.00[EUR][1000 genomes]
rs73604081	1.00[EUR][1000 genomes]
rs74127112	1.00[EUR][1000 genomes]
rs74127134	1.00[EUR][1000 genomes]
rs74127135	1.00[EUR][1000 genomes]
rs74127138	1.00[EUR][1000 genomes]
rs74127139	1.00[EUR][1000 genomes]
rs74127142	1.00[EUR][1000 genomes]
rs74127147	1.00[EUR][1000 genomes]
rs74127152	1.00[EUR][1000 genomes]
rs74127165	1.00[EUR][1000 genomes]
rs74127175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7893159	1.00[EUR][1000 genomes]
rs7895005	1.00[EUR][1000 genomes]
rs7895017	1.00[EUR][1000 genomes]
rs7899126	1.00[EUR][1000 genomes]
rs7910182	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv894987	chr10:28165502-28326775	ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831815	chr10:28235661-28407533	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1052182	chr10:28259142-28361830	Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28239800-28287200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:28286200-28288000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:28286400-28287000	Bivalent/Poised TSS	Fetal Brain Male	brain
4	chr10:28286600-28287000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
5	chr10:28286600-28287000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr10:28286600-28287600	Active TSS	Primary B cells from cord blood	blood
7	chr10:28286600-28287600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr10:28286600-28288000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr10:28286600-28288200	Flanking Active TSS	Liver	Liver
10	chr10:28286600-28288400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:28286600-28288400	Active TSS	Stomach Smooth Muscle	stomach
12	chr10:28286600-28288600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr10:28286600-28288600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr10:28286800-28287000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
15	chr10:28286800-28287000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr10:28286800-28287000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:28286800-28287000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr10:28286800-28287000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:28286800-28287000	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr10:28286800-28287000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr10:28286800-28287000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
22	chr10:28286800-28287000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
23	chr10:28286800-28287000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:28286800-28287000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:28286800-28287000	Active TSS	Brain Cingulate Gyrus	brain
26	chr10:28286800-28287000	Enhancers	Brain Germinal Matrix	brain
27	chr10:28286800-28287000	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr10:28286800-28287000	Bivalent Enhancer	Fetal Heart	heart
29	chr10:28286800-28287000	Flanking Active TSS	Fetal Lung	lung
30	chr10:28286800-28287000	Enhancers	Pancreas	Pancrea
31	chr10:28286800-28287000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr10:28286800-28287000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
33	chr10:28286800-28287000	Bivalent/Poised TSS	NHDF-Ad	bronchial
34	chr10:28286800-28287200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
35	chr10:28286800-28287200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr10:28286800-28287200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr10:28286800-28287400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr10:28286800-28287400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr10:28286800-28287400	Flanking Active TSS	HUVEC	blood vessel
40	chr10:28286800-28287400	Flanking Bivalent TSS/Enh	Osteobl	bone
41	chr10:28286800-28287800	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr10:28286800-28287800	Flanking Bivalent TSS/Enh	Dnd41	blood
43	chr10:28286800-28288000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:28286800-28288000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:28286800-28288000	Active TSS	Brain Substantia Nigra	brain
46	chr10:28286800-28288000	Active TSS	Colon Smooth Muscle	Colon
47	chr10:28286800-28288000	Active TSS	Fetal Stomach	stomach
48	chr10:28286800-28288200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr10:28286800-28288200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:28286800-28288200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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