Variant report

Variant	rs58052353
Chromosome Location	chr10:43977327-43977328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43902685..43904654-chr10:43976459..43978069,2	MCF-7	breast:
2	chr10:43971469..43973705-chr10:43977289..43979716,2	K562	blood:
3	chr10:43930707..43932404-chr10:43975241..43977746,2	K562	blood:
4	chr10:43976615..43979208-chr10:43982214..43983793,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FXYD4-4	chr10:43976877-43978007	NR_026693

Variant related genes	Relation type
ENSG00000243660	Chromatin interaction
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12570790	0.90[AFR][1000 genomes]
rs12571914	0.90[AFR][1000 genomes]
rs55659835	0.90[AFR][1000 genomes]
rs55957438	0.89[AFR][1000 genomes]
rs55969732	1.00[EUR][1000 genomes]
rs55984046	1.00[EUR][1000 genomes]
rs56067782	1.00[EUR][1000 genomes]
rs56305563	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56706302	1.00[EUR][1000 genomes]
rs57050417	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57169447	1.00[EUR][1000 genomes]
rs58036139	1.00[EUR][1000 genomes]
rs58345794	1.00[EUR][1000 genomes]
rs58594005	1.00[EUR][1000 genomes]
rs58829593	0.89[AFR][1000 genomes]
rs59615405	1.00[AFR][1000 genomes]
rs59737279	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59770090	0.90[AFR][1000 genomes]
rs59946114	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60057912	0.90[AFR][1000 genomes]
rs60274910	0.90[AFR][1000 genomes]
rs61859048	0.90[AFR][1000 genomes]
rs61859049	0.90[AFR][1000 genomes]
rs61859050	0.90[AFR][1000 genomes]
rs61859051	0.90[AFR][1000 genomes]
rs61859052	1.00[AFR][1000 genomes]
rs61859058	0.90[AFR][1000 genomes]
rs61859967	0.90[AFR][1000 genomes]
rs61859968	0.90[AFR][1000 genomes]
rs73267969	1.00[EUR][1000 genomes]
rs74135720	1.00[EUR][1000 genomes]
rs74135736	1.00[EUR][1000 genomes]
rs74137729	1.00[EUR][1000 genomes]
rs74137730	1.00[EUR][1000 genomes]
rs74137733	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74137734	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74137735	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74137736	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74137737	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74137738	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74137739	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74137740	0.89[AFR][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	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1046236	chr10:43968075-44012933	ZNF genes & repeats Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43967400-43978600	Weak transcription	Pancreas	Pancrea
2	chr10:43969800-43978200	Weak transcription	Fetal Kidney	kidney
3	chr10:43974800-43982600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:43976000-43979200	ZNF genes & repeats	Liver	Liver
5	chr10:43976200-43978600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:43976200-43978600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:43976200-43978600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr10:43976200-43978800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr10:43976400-43977400	ZNF genes & repeats	Thymus	Thymus
10	chr10:43976400-43977600	ZNF genes & repeats	Aorta	Aorta
11	chr10:43976400-43978000	ZNF genes & repeats	Colon Smooth Muscle	Colon
12	chr10:43976400-43978200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:43976400-43978400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:43976400-43978400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
15	chr10:43976400-43978400	ZNF genes & repeats	Adipose Nuclei	Adipose
16	chr10:43976400-43978600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr10:43976400-43978600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:43976400-43978600	ZNF genes & repeats	Ovary	ovary
19	chr10:43976400-43978800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:43976600-43978200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
21	chr10:43976600-43978600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
22	chr10:43976800-43977600	ZNF genes & repeats	Fetal Muscle Leg	muscle
23	chr10:43976800-43977800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:43976800-43978000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
25	chr10:43976800-43978000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
26	chr10:43976800-43978200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
27	chr10:43977000-43977400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:43977000-43977400	ZNF genes & repeats	Osteobl	bone
29	chr10:43977000-43977600	Strong transcription	Brain Anterior Caudate	brain
30	chr10:43977000-43977800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
31	chr10:43977000-43977800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
32	chr10:43977000-43978400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
33	chr10:43977000-43979000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
34	chr10:43977200-43977400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
35	chr10:43977200-43977400	ZNF genes & repeats	Gastric	stomach
36	chr10:43977200-43977400	ZNF genes & repeats	HSMM	muscle
37	chr10:43977200-43977600	ZNF genes & repeats	Right Ventricle	heart
38	chr10:43977200-43977800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
39	chr10:43977200-43978000	ZNF genes & repeats	Brain Substantia Nigra	brain
40	chr10:43977200-43978200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
41	chr10:43977200-43978200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
42	chr10:43977200-43978400	ZNF genes & repeats	Left Ventricle	heart
43	chr10:43977200-43978400	ZNF genes & repeats	Psoas Muscle	Psoas
44	chr10:43977200-43978600	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr10:43977200-43978600	ZNF genes & repeats	Brain Angular Gyrus	brain
46	chr10:43977200-43978600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
47	chr10:43977200-43978600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
48	chr10:43977200-43978600	ZNF genes & repeats	Fetal Lung	lung
49	chr10:43977200-43978600	ZNF genes & repeats	HSMMtube	muscle
50	chr10:43977200-43978800	ZNF genes & repeats	Brain Hippocampus Middle	brain

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