Variant report

Variant	rs62109251
Chromosome Location	chr19:52737836-52737837
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	POLR2A	chr19:52737496-52737908	U87	brain:	n/a	n/a
2	POLR2A	chr19:52737735-52738738	A549	lung:	n/a	n/a
3	POLR2A	chr19:52737641-52738320	HepG2	liver:	n/a	n/a
4	FOXA2	chr19:52737734-52737911	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:52737551-52737908	U87	brain:	n/a	n/a
6	POLR2A	chr19:52737761-52737943	MCF10A-Er-Src	breast:	n/a	n/a
7	ARID3A	chr19:52737625-52738018	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:52737730-52737965	HCT-116	colon:	n/a	n/a
9	POLR2A	chr19:52737509-52738729	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52732749..52736646-chr19:52736909..52741775,7	K562	blood:
2	chr19:52725400..52727782-chr19:52737067..52738597,2	K562	blood:

Variant related genes	Relation type
ENSG00000268015	TF binding region
ENSG00000268015	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10520481	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16983537	0.87[EUR][1000 genomes]
rs16983625	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16983630	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55955399	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58194802	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62109201	0.87[EUR][1000 genomes]
rs62109202	0.87[EUR][1000 genomes]
rs62109205	0.90[EUR][1000 genomes]
rs62109208	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62109210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62109247	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62109248	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62109249	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62109250	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62109254	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62109256	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7251497	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73575024	0.88[EUR][1000 genomes]
rs73575040	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8101929	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv962989	chr19:52732337-52742183	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52730800-52741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:52731600-52738000	Weak transcription	Fetal Brain Male	brain
3	chr19:52731600-52741000	Weak transcription	Colon Smooth Muscle	Colon
4	chr19:52732000-52740600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:52732000-52740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:52732200-52741000	Weak transcription	Dnd41	blood
7	chr19:52732200-52741200	Weak transcription	Fetal Lung	lung
8	chr19:52732400-52740200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:52732400-52740600	Weak transcription	Brain Angular Gyrus	brain
10	chr19:52732400-52741000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr19:52732400-52741200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr19:52733200-52742800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:52733200-52759600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:52733400-52741200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr19:52734200-52741000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:52734400-52751600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:52734600-52740800	Weak transcription	Fetal Stomach	stomach
18	chr19:52734600-52743800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:52735000-52740400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:52735200-52738800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:52735200-52740600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:52735200-52741200	Weak transcription	Fetal Muscle Leg	muscle
23	chr19:52737800-52738000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr19:52737800-52738400	Enhancers	HepG2	liver

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