Variant report

Variant	rs446016
Chromosome Location	chr19:44501518-44501519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44501460..44503364-chr19:44505726..44508056,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF45-2	chr19:44501048-44503384	ENSG00000266921.1
2	lnc-ZNF45-2	chr19:44501048-44502536	NONHSAT066650
3	lnc-ZNF45-2	chr19:44501051-44501947	ENSG00000266921.1

Variant related genes	Relation type
ENSG00000159882	Chromatin interaction
ENSG00000266921	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs35292176	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56101767	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs446016	ZNF223	cis	Thyroid	GTEx
rs446016	ZNF155	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44489200-44506200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr19:44489200-44506200	Weak transcription	Hela-S3	cervix
3	chr19:44489600-44506200	Weak transcription	HepG2	liver
4	chr19:44491000-44501600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr19:44491000-44503400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:44491000-44503800	ZNF genes & repeats	Liver	Liver
7	chr19:44491400-44503400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr19:44491600-44501800	Strong transcription	Brain Hippocampus Middle	brain
9	chr19:44491800-44502200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:44492000-44502000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:44492400-44501800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr19:44492400-44501800	Strong transcription	Brain Cingulate Gyrus	brain
13	chr19:44492400-44502000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:44492400-44502200	Strong transcription	Fetal Intestine Large	intestine
15	chr19:44492400-44502200	Strong transcription	HSMM	muscle
16	chr19:44492400-44502400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:44492400-44502400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:44492400-44502600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr19:44492600-44501600	Strong transcription	Thymus	Thymus
20	chr19:44492600-44502000	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:44492600-44502200	Strong transcription	Dnd41	blood
22	chr19:44492600-44502400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:44492600-44502400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:44492600-44502600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:44492800-44502000	Strong transcription	Brain Substantia Nigra	brain
26	chr19:44492800-44502000	Strong transcription	Fetal Thymus	thymus
27	chr19:44492800-44502000	Strong transcription	HSMMtube	muscle
28	chr19:44492800-44502200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:44493000-44501600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:44493200-44501800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:44493200-44501800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:44493200-44501800	Strong transcription	Placenta	Placenta
33	chr19:44493200-44501800	Strong transcription	Fetal Stomach	stomach
34	chr19:44493200-44502200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:44493400-44501600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:44493400-44501800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:44493400-44502000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:44493400-44502400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:44493600-44502200	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr19:44494400-44502000	Strong transcription	Right Ventricle	heart
41	chr19:44496600-44503200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
42	chr19:44496600-44506200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:44497000-44506400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:44497000-44506600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:44498400-44502400	Strong transcription	Psoas Muscle	Psoas
46	chr19:44498600-44502000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
47	chr19:44498800-44501600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
48	chr19:44498800-44502000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
49	chr19:44499000-44502000	ZNF genes & repeats	Pancreas	Pancrea
50	chr19:44499000-44502400	ZNF genes & repeats	Fetal Intestine Small	intestine

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