Variant report

Variant	rs62121654
Chromosome Location	chr19:56990010-56990011
allele	C/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	POLR2A	chr19:56987970-56990186	IMR90	lung:	n/a	n/a
2	MXI1	chr19:56987781-56990043	IMR90	lung:	n/a	n/a
3	KAP1	chr19:56989097-56990085	HEK293	kidney:	n/a	n/a
4	MAX	chr19:56988074-56990138	SK-N-SH	brain:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56989847-56989857 chr19:56988525-56988534 chr19:56988774-56988783
5	MAZ	chr19:56987654-56990331	IMR90	lung:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56989847-56989857 chr19:56988525-56988534 chr19:56988774-56988783
6	SIN3A	chr19:56988034-56990073	H1-hESC	embryonic stem cell:	n/a	chr19:56989351-56989364 chr19:56988699-56988708 chr19:56989198-56989209 chr19:56988812-56988823
7	MXI1	chr19:56987494-56990858	SK-N-SH	brain:	n/a	n/a
8	CEBPB	chr19:56989289-56990099	IMR90	lung:	n/a	chr19:56989652-56989661 chr19:56989652-56989661 chr19:56989652-56989661
9	POLR2A	chr19:56987976-56990044	HL-60	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC004696.1-1	chr19:56988619-56990056	ENSG00000166770.6

Variant related genes	Relation type
ZNF667	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs60141587	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62121652	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62122961	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv3358424	chr19:56987565-56990113	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56985400-56990400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:56985400-56991400	ZNF genes & repeats	Liver	Liver
3	chr19:56987000-56990400	ZNF genes & repeats	Gastric	stomach
4	chr19:56987400-56990800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:56987400-56992400	ZNF genes & repeats	Lung	lung
6	chr19:56987600-56990200	ZNF genes & repeats	Spleen	Spleen
7	chr19:56987600-56990600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:56987600-56990600	Active TSS	Brain Anterior Caudate	brain
9	chr19:56987600-56990800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr19:56987600-56990800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr19:56987600-56991000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:56987600-56991200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:56987800-56990200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:56987800-56990400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:56987800-56990400	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr19:56987800-56990400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr19:56987800-56990400	Active TSS	Fetal Muscle Trunk	muscle
18	chr19:56987800-56990400	Active TSS	Rectal Smooth Muscle	rectum
19	chr19:56987800-56990400	Active TSS	NHDF-Ad	bronchial
20	chr19:56987800-56990600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
21	chr19:56987800-56990600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:56987800-56990600	ZNF genes & repeats	Colonic Mucosa	Colon
23	chr19:56987800-56990600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr19:56988000-56990200	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr19:56988000-56990200	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr19:56988000-56990200	Active TSS	HUVEC	blood vessel
27	chr19:56988000-56990400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr19:56988000-56990400	Active TSS	Fetal Intestine Large	intestine
29	chr19:56988000-56990600	Active TSS	Brain Cingulate Gyrus	brain
30	chr19:56988000-56990600	Active TSS	Fetal Brain Female	brain
31	chr19:56988000-56990600	Active TSS	Psoas Muscle	Psoas
32	chr19:56988000-56990600	Active TSS	HSMM	muscle
33	chr19:56988000-56990600	Active TSS	HSMMtube	muscle
34	chr19:56988000-56990600	Active TSS	NH-A	brain
35	chr19:56988000-56991000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:56988000-56991000	Active TSS	Muscle Satellite Cultured Cells	--
37	chr19:56988200-56990200	Active TSS	Aorta	Aorta
38	chr19:56988200-56990200	Active TSS	Left Ventricle	heart
39	chr19:56988200-56990400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:56988200-56990400	Active TSS	Fetal Intestine Small	intestine
41	chr19:56988200-56990800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr19:56988200-56990800	Active TSS	Fetal Kidney	kidney
43	chr19:56988200-56991000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:56988200-56991000	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr19:56988400-56990400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr19:56988400-56990400	Active TSS	Fetal Lung	lung
47	chr19:56988400-56990400	Active TSS	Fetal Stomach	stomach
48	chr19:56988400-56990400	Active TSS	Ovary	ovary
49	chr19:56988400-56990400	Active TSS	NHEK	skin
50	chr19:56988400-56990400	Active TSS	NHLF	lung

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