Variant report

Variant	rs58997200
Chromosome Location	chr19:56892376-56892377
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	chr19:56892259-56892464	K562	blood:	n/a	n/a
2	POLR2A	chr19:56891538-56892631	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:56891565-56892756	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56890954..56893451-chr19:56903592..56906297,2	K562	blood:

Variant related genes	Relation type
ENSG00000267459	TF binding region
ENSG00000267776	TF binding region
ENSG00000018869	Chromatin interaction
ENSG00000267454	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs60628802	1.00[AMR][1000 genomes]
rs61079647	1.00[AMR][1000 genomes]
rs61389610	1.00[AMR][1000 genomes]
rs7247773	1.00[AMR][1000 genomes]
rs7257563	1.00[AMR][1000 genomes]
rs73618178	1.00[AMR][1000 genomes]
rs73618195	1.00[AMR][1000 genomes]
rs73618201	1.00[AMR][1000 genomes]
rs73621209	1.00[AMR][1000 genomes]
rs73626790	1.00[AMR][1000 genomes]
rs73628710	1.00[AMR][1000 genomes]
rs73628723	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56881200-56904000	ZNF genes & repeats	Liver	Liver
2	chr19:56881400-56893000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:56884000-56892600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:56884600-56892400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:56884800-56892400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:56888800-56892800	Weak transcription	Colonic Mucosa	Colon
7	chr19:56889200-56897400	Weak transcription	Gastric	stomach
8	chr19:56889200-56901200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:56889200-56904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:56889400-56895200	Weak transcription	Brain Angular Gyrus	brain
11	chr19:56889400-56895400	Weak transcription	Brain Substantia Nigra	brain
12	chr19:56889400-56895600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:56889400-56904000	Weak transcription	Fetal Heart	heart
14	chr19:56889400-56904000	Weak transcription	K562	blood
15	chr19:56890000-56894400	Weak transcription	Brain Anterior Caudate	brain
16	chr19:56890000-56900200	Weak transcription	Right Ventricle	heart
17	chr19:56890200-56892400	Strong transcription	Fetal Brain Female	brain
18	chr19:56890200-56894200	Weak transcription	Brain Germinal Matrix	brain
19	chr19:56890200-56895200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:56890200-56895400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:56890200-56903600	Weak transcription	Fetal Brain Male	brain
22	chr19:56890400-56894400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:56890600-56893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:56890600-56894000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:56890600-56894600	Weak transcription	Fetal Kidney	kidney
26	chr19:56890600-56895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:56890600-56900200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:56890600-56900400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:56890600-56904000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:56890800-56894200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:56890800-56894400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:56890800-56895200	Weak transcription	Psoas Muscle	Psoas
33	chr19:56890800-56895600	Weak transcription	Left Ventricle	heart
34	chr19:56891000-56892400	ZNF genes & repeats	Fetal Lung	lung
35	chr19:56891200-56895000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:56891200-56895400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:56891600-56893200	ZNF genes & repeats	Adipose Nuclei	Adipose
38	chr19:56891600-56893200	ZNF genes & repeats	Aorta	Aorta
39	chr19:56891800-56892400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:56892000-56892400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:56892000-56894400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:56892000-56894800	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:56892000-56894800	Weak transcription	Stomach Smooth Muscle	stomach

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