Variant report

Variant	rs10420143
Chromosome Location	chr19:44608082-44608083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44514794..44516383-chr19:44607631..44609191,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10406335	0.88[EUR][1000 genomes]
rs10410306	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413195	0.87[EUR][1000 genomes]
rs2061332	0.93[ASN][1000 genomes]
rs2061333	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2068061	0.85[EUR][1000 genomes]
rs2168778	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2284978	0.83[EUR][1000 genomes]
rs2284980	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2356750	0.82[EUR][1000 genomes]
rs28446946	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28539456	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3172	0.97[ASN][1000 genomes]
rs3200505	0.93[ASN][1000 genomes]
rs3746319	0.93[ASN][1000 genomes]
rs3746321	0.93[ASN][1000 genomes]
rs4239529	0.84[EUR][1000 genomes]
rs4508518	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4802204	0.96[ASN][1000 genomes]
rs4802205	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4802206	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802207	1.00[ASN][1000 genomes]
rs4803676	0.85[EUR][1000 genomes]
rs4803678	0.84[EUR][1000 genomes]
rs4803679	0.84[EUR][1000 genomes]
rs4803680	0.84[EUR][1000 genomes]
rs4803681	0.97[ASN][1000 genomes]
rs55876899	0.92[ASN][1000 genomes]
rs56353321	0.94[ASN][1000 genomes]
rs62115524	0.94[ASN][1000 genomes]
rs62115526	1.00[ASN][1000 genomes]
rs6509141	0.83[EUR][1000 genomes]
rs7249827	0.84[EUR][1000 genomes]
rs7249834	0.84[EUR][1000 genomes]
rs7250004	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250005	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250076	0.84[EUR][1000 genomes]
rs7250171	0.84[EUR][1000 genomes]
rs7251868	0.83[EUR][1000 genomes]
rs7508149	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7508762	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8101657	0.84[EUR][1000 genomes]
rs8104573	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105860	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8108021	0.94[ASN][1000 genomes]
rs8108404	0.97[ASN][1000 genomes]
rs8113750	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304638	0.88[EUR][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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10420143	ZNF223	cis	Thyroid	GTEx
rs10420143	ZNF223	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44599600-44609000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44599600-44610600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:44599600-44611000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:44599800-44609200	Weak transcription	NHEK	skin
5	chr19:44599800-44610400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:44600000-44610400	Weak transcription	Stomach Mucosa	stomach
7	chr19:44600400-44608200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:44600400-44610400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:44600400-44610600	Strong transcription	HSMM	muscle
10	chr19:44600400-44616200	ZNF genes & repeats	Liver	Liver
11	chr19:44600600-44608600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:44600600-44608800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr19:44600800-44608400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr19:44600800-44608600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:44600800-44609000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:44600800-44609000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr19:44600800-44609200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr19:44600800-44610400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:44600800-44610400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:44600800-44610600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:44600800-44610600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr19:44600800-44612800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:44600800-44614000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:44600800-44614600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:44601000-44608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:44601000-44608200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:44601000-44608400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:44601000-44609000	Strong transcription	Left Ventricle	heart
29	chr19:44601000-44609200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:44601000-44609400	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr19:44601000-44610600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:44601000-44611600	Strong transcription	Fetal Thymus	thymus
33	chr19:44601400-44608400	Strong transcription	Colon Smooth Muscle	Colon
34	chr19:44601400-44608600	Strong transcription	Brain Anterior Caudate	brain
35	chr19:44601400-44608800	Strong transcription	Brain Substantia Nigra	brain
36	chr19:44601400-44609400	Strong transcription	Brain Hippocampus Middle	brain
37	chr19:44601400-44611000	Strong transcription	Placenta	Placenta
38	chr19:44601800-44608600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:44601800-44608800	Strong transcription	Osteobl	bone
40	chr19:44601800-44609400	Strong transcription	Brain Cingulate Gyrus	brain
41	chr19:44602000-44609400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:44602000-44610400	Strong transcription	Dnd41	blood
43	chr19:44602200-44608200	Strong transcription	Primary B cells from cord blood	blood
44	chr19:44602200-44608200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:44602200-44608200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:44603600-44608400	Strong transcription	A549	lung
47	chr19:44604000-44608400	Strong transcription	Fetal Kidney	kidney
48	chr19:44604200-44608400	Strong transcription	Fetal Brain Female	brain
49	chr19:44604200-44610400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:44604200-44610400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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