Variant report

Variant	rs62109202
Chromosome Location	chr19:52694651-52694652
allele	G/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52641405..52644253-chr19:52691691..52696539,6	MCF-7	breast:
2	chr19:52692900..52696088-chr19:52702014..52707428,7	MCF-7	breast:
3	chr19:52597423..52599077-chr19:52692134..52694986,2	K562	blood:
4	chr1:17221697..17224418-chr19:52692331..52695072,2	MCF-7	breast:
5	chr19:52638083..52640348-chr19:52693399..52695139,2	MCF-7	breast:
6	chr19:52641479..52644491-chr19:52690575..52695402,7	MCF-7	breast:
7	chr19:52692960..52694798-chr19:52714697..52716755,2	K562	blood:
8	chr19:52671404..52675593-chr19:52690586..52694996,6	MCF-7	breast:
9	chr19:52642060..52644482-chr19:52693480..52696819,3	K562	blood:
10	chr19:52693832..52696719-chr19:52708763..52711049,3	MCF-7	breast:
11	chr19:52691998..52694919-chr19:53605403..53608321,3	K562	blood:
12	chr19:52692325..52695090-chr19:52733176..52735417,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268015	Chromatin interaction
ENSG00000170949	Chromatin interaction
ENSG00000267827	Chromatin interaction
ENSG00000267927	Chromatin interaction
ENSG00000196267	Chromatin interaction
ENSG00000207005	Chromatin interaction
ENSG00000256087	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000197608	Chromatin interaction
ENSG00000105568	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10520481	0.90[EUR][1000 genomes]
rs16983537	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16983625	0.85[EUR][1000 genomes]
rs16983630	0.85[EUR][1000 genomes]
rs55955399	0.90[EUR][1000 genomes]
rs58194802	0.85[EUR][1000 genomes]
rs62109201	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62109205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62109208	0.90[EUR][1000 genomes]
rs62109210	0.90[EUR][1000 genomes]
rs62109247	0.92[EUR][1000 genomes]
rs62109248	0.89[EUR][1000 genomes]
rs62109249	0.89[EUR][1000 genomes]
rs62109250	0.85[EUR][1000 genomes]
rs62109251	0.87[EUR][1000 genomes]
rs62109254	0.85[EUR][1000 genomes]
rs7251497	0.85[EUR][1000 genomes]
rs73575024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73575040	0.90[EUR][1000 genomes]
rs8101929	0.90[EUR][1000 genomes]
rs8107383	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv21017	chr19:52692555-52696215	Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52692000-52694800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:52692000-52694800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:52692000-52695400	Active TSS	Left Ventricle	heart
4	chr19:52692200-52694800	Active TSS	Lung	lung
5	chr19:52692200-52694800	Active TSS	Ovary	ovary
6	chr19:52692400-52695400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:52693800-52695000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr19:52693800-52695200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr19:52694000-52694800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr19:52694000-52694800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr19:52694000-52694800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:52694000-52694800	Flanking Active TSS	Thymus	Thymus
13	chr19:52694000-52695000	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr19:52694000-52695000	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr19:52694000-52695000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:52694000-52695000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr19:52694000-52695000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:52694000-52695000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr19:52694000-52695000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr19:52694000-52695200	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr19:52694000-52695200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:52694000-52695200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:52694200-52694800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr19:52694200-52694800	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr19:52694200-52694800	Flanking Active TSS	Colonic Mucosa	Colon
26	chr19:52694200-52694800	Flanking Active TSS	Fetal Thymus	thymus
27	chr19:52694200-52695000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr19:52694200-52695000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr19:52694200-52695000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr19:52694200-52695000	Flanking Active TSS	HUVEC	blood vessel
31	chr19:52694200-52695200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr19:52694200-52695200	Flanking Active TSS	Liver	Liver
33	chr19:52694200-52695200	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr19:52694200-52695200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr19:52694200-52695200	Flanking Active TSS	Fetal Brain Male	brain
36	chr19:52694200-52695200	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr19:52694200-52695200	Flanking Active TSS	Right Atrium	heart
38	chr19:52694200-52695400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:52694200-52695400	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr19:52694200-52695400	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr19:52694200-52695400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr19:52694200-52695400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr19:52694200-52695600	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr19:52694200-52695600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr19:52694200-52695600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr19:52694400-52694800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
47	chr19:52694400-52694800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:52694400-52694800	Flanking Active TSS	Esophagus	oesophagus
49	chr19:52694400-52694800	Flanking Active TSS	Fetal Kidney	kidney
50	chr19:52694400-52694800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle

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