Variant report

Variant	rs58339212
Chromosome Location	chr19:21861075-21861076
allele	G/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	CTCF	chr19:21861031-21861289	H1-hESC	embryonic stem cell:	n/a	chr19:21861252-21861273
2	RAD21	chr19:21861042-21861303	H1-hESC	embryonic stem cell:	n/a	chr19:21861136-21861150 chr19:21861194-21861206
3	CTCF	chr19:21861040-21861190	WERI-Rb-1	eye:	n/a	n/a
4	RAD21	chr19:21860912-21861415	H1-hESC	embryonic stem cell:	n/a	chr19:21861136-21861150 chr19:21861194-21861206
5	RAD21	chr19:21860929-21861253	H1-hESC	embryonic stem cell:	n/a	chr19:21861136-21861150 chr19:21861194-21861206
6	CTCF	chr19:21861044-21861298	H1-hESC	embryonic stem cell:	n/a	chr19:21861252-21861273

Variant related genes	Relation type
ENSG00000268433	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12232782	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12232857	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461057	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461755	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461975	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12463094	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2139534	0.82[ASN][1000 genomes]
rs58621185	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58919976	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59571905	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59724594	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60312928	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61517956	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253108	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7258332	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73546506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101178	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8101397	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	esv3392559	chr19:21798396-21965956	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv2760530	chr19:21798427-21885936	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
11	nsv963135	chr19:21800743-21892052	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv833783	chr19:21821406-21991838	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	esv1815274	chr19:21825750-21981855	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription 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	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21859200-21861600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr19:21859400-21861200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:21860400-21861200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
4	chr19:21860400-21861200	Active TSS	Primary T cells from cord blood	blood
5	chr19:21860400-21861200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:21860400-21861200	Active TSS	Fetal Intestine Small	intestine
7	chr19:21860400-21861400	Active TSS	Thymus	Thymus
8	chr19:21860600-21861200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:21860600-21861200	Enhancers	Primary B cells from peripheral blood	blood
10	chr19:21860600-21861200	ZNF genes & repeats	Pancreas	Pancrea
11	chr19:21860600-21861400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
12	chr19:21860800-21861200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr19:21860800-21861200	Active TSS	Primary hematopoietic stem cells	blood
14	chr19:21860800-21861200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr19:21860800-21861200	Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr19:21860800-21861200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:21860800-21861200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
18	chr19:21860800-21861200	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr19:21860800-21861200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
20	chr19:21860800-21861200	Active TSS	Right Ventricle	heart
21	chr19:21860800-21861400	Active TSS	Dnd41	blood
22	chr19:21861000-21861200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr19:21861000-21861200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr19:21861000-21861200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
25	chr19:21861000-21861200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
26	chr19:21861000-21861400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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