Variant report

Variant	rs74086906
Chromosome Location	chr12:49994658-49994659
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49979616..49982528-chr12:49994555..49996212,2	MCF-7	breast:
2	chr12:49993213..49995668-chr12:49998189..50000775,3	K562	blood:
3	chr12:49994568..49996559-chr12:50008770..50010763,2	K562	blood:
4	chr12:49989096..49991306-chr12:49994461..49996407,2	K562	blood:
5	chr12:49993836..49997498-chr12:50014878..50017386,3	K562	blood:
6	chr12:49960315..49962480-chr12:49993322..49995583,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNH3-1	chr12:49993609-49994926	ENSG00000250952
2	lnc-KCNH3-1	chr12:49993719-49994811	ENSG00000250952
3	lnc-FAM186B-2	chr12:49993252-49994917	NR_027450

No data

Variant related genes	Relation type
ENSG00000110844	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000135436	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs4641552	0.87[AFR][1000 genomes]
rs55637397	0.90[AFR][1000 genomes]
rs57398316	1.00[EUR][1000 genomes]
rs60415769	0.87[AFR][1000 genomes]
rs60613973	0.83[AFR][1000 genomes]
rs61281663	0.81[AFR][1000 genomes]
rs74086911	0.90[AFR][1000 genomes]
rs74087196	1.00[EUR][1000 genomes]
rs74089556	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	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
2	chr12:49977600-49996200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:49979600-50002600	Weak transcription	HepG2	liver
4	chr12:49979800-49995600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:49979800-49998800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:49980400-50000200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:49982600-50015400	Weak transcription	Pancreas	Pancrea
8	chr12:49982800-49996000	Weak transcription	Brain Angular Gyrus	brain
9	chr12:49983000-49996000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:49983200-49995000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:49983200-49999400	Weak transcription	HSMMtube	muscle
12	chr12:49983200-50002800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:49983400-49994800	Weak transcription	HSMM	muscle
14	chr12:49983400-50002800	Weak transcription	NHEK	skin
15	chr12:49985000-49994800	Weak transcription	Ovary	ovary
16	chr12:49985200-49998600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:49985200-49998600	Weak transcription	Placenta	Placenta
18	chr12:49985200-50003000	Weak transcription	Lung	lung
19	chr12:49985400-49996200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:49985400-49997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:49985400-49998000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:49985600-49995800	Weak transcription	Thymus	Thymus
23	chr12:49985600-49998800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:49985800-49998400	Weak transcription	Fetal Lung	lung
25	chr12:49987200-49998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:49990600-49998400	Weak transcription	Fetal Heart	heart
27	chr12:49991800-49996800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:49992000-49995000	Strong transcription	Fetal Stomach	stomach
29	chr12:49992200-49995200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:49992800-49995000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:49992800-49996000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:49992800-50003200	Weak transcription	Fetal Intestine Large	intestine
33	chr12:49993000-49995200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:49993200-49995000	Strong transcription	Fetal Intestine Small	intestine
35	chr12:49993200-49995400	Strong transcription	Fetal Muscle Leg	muscle
36	chr12:49993400-49994800	Strong transcription	Fetal Brain Female	brain
37	chr12:49993600-49994800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:49993600-49995200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:49993800-49995000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:49993800-49995000	Strong transcription	Primary T cells from cord blood	blood
41	chr12:49993800-49995000	Strong transcription	Brain Germinal Matrix	brain
42	chr12:49994000-49994800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:49994000-49995000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:49994000-49995000	Strong transcription	Brain Hippocampus Middle	brain
45	chr12:49994000-50002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:49994400-49995000	Strong transcription	Right Ventricle	heart
47	chr12:49994400-50002800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:49994400-50003200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:49994400-50004400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:49994600-49996000	Weak transcription	Stomach Smooth Muscle	stomach

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