Variant report

Variant	rs12972251
Chromosome Location	chr19:56912151-56912152
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	CBX3	chr19:56911845-56912230	K562	blood:	n/a	n/a
2	SETDB1	chr19:56911713-56912422	U2OS	brain:	n/a	n/a
3	KAP1	chr19:56911766-56912258	HEK293	kidney:	n/a	n/a
4	KAP1	chr19:56911511-56912279	K562	blood:	n/a	n/a
5	CBX3	chr19:56911863-56912213	K562	blood:	n/a	n/a
6	TRIM28	chr19:56911924-56912187	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56902006..56908060-chr19:56909612..56917978,15	K562	blood:
2	chr19:56910743..56913203-chr19:56914097..56915659,2	K562	blood:

Variant related genes	Relation type
ZNF583	TF binding region
ENSG00000266631	TF binding region
ENSG00000267454	Chromatin interaction
ENSG00000198440	Chromatin interaction
ENSG00000018869	Chromatin interaction
ENSG00000266631	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11878390	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12980022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34450526	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35421936	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36090893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][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	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
7	nsv544096	chr19:56905651-56933455	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56905000-56913600	ZNF genes & repeats	Liver	Liver
2	chr19:56905600-56914600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:56905800-56914400	Weak transcription	Fetal Heart	heart
4	chr19:56908000-56913600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:56908000-56913600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:56908000-56914800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:56908200-56912400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
8	chr19:56908200-56913000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr19:56908200-56914600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:56908400-56913600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:56908600-56912200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:56908600-56913400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
13	chr19:56908800-56913600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr19:56908800-56913600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
15	chr19:56909000-56913600	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr19:56909200-56912200	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:56909200-56913400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr19:56909400-56912400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:56909400-56913600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr19:56910000-56914200	ZNF genes & repeats	Dnd41	blood
21	chr19:56910200-56914000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:56910400-56912200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:56910400-56913400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:56910400-56914600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr19:56910600-56914200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr19:56910600-56914200	Weak transcription	Brain Anterior Caudate	brain
27	chr19:56910600-56914400	Weak transcription	Brain Substantia Nigra	brain
28	chr19:56910600-56914400	Weak transcription	Fetal Brain Male	brain
29	chr19:56910800-56914400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr19:56910800-56914600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:56911000-56914200	Weak transcription	Brain Angular Gyrus	brain
32	chr19:56911000-56914400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:56911000-56914400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:56911000-56914600	Weak transcription	Ovary	ovary
35	chr19:56911000-56914600	Weak transcription	Right Ventricle	heart
36	chr19:56911000-56914800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr19:56911000-56915000	Weak transcription	Aorta	Aorta
38	chr19:56911200-56913000	Weak transcription	HSMMtube	muscle
39	chr19:56911200-56914400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr19:56911400-56912200	ZNF genes & repeats	Fetal Kidney	kidney
41	chr19:56911400-56914200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:56911600-56912200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:56911800-56912200	ZNF genes & repeats	Left Ventricle	heart
44	chr19:56911800-56912200	Weak transcription	Stomach Mucosa	stomach
45	chr19:56912000-56912600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:56912000-56914200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:56912000-56914200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:56912000-56914400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:56912000-56914400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:56912000-56914400	Weak transcription	Brain Cingulate Gyrus	brain

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