Variant report

Variant	rs6509141
Chromosome Location	chr19:44613119-44613120
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	chr19:44612970-44614091	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44611647..44614063-chr19:44614697..44617156,2	K562	blood:
2	chr17:58602968..58604763-chr19:44611791..44613959,2	MCF-7	breast:
3	chr19:44611565..44614380-chr19:44615671..44618988,4	MCF-7	breast:
4	chr19:44599467..44601264-chr19:44610771..44613313,2	MCF-7	breast:

Variant related genes	Relation type
ZNF225	TF binding region
ENSG00000186019	Chromatin interaction
ENSG00000256294	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000267680	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10410306	0.83[EUR][1000 genomes]
rs10420143	0.83[EUR][1000 genomes]
rs2068061	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2284978	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300962	0.85[ASN][1000 genomes]
rs28446946	0.82[EUR][1000 genomes]
rs28539456	0.82[EUR][1000 genomes]
rs4239529	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4429390	0.93[ASN][1000 genomes]
rs4459653	0.93[ASN][1000 genomes]
rs4802206	0.83[EUR][1000 genomes]
rs4803674	0.80[CEU][hapmap]
rs4803676	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803677	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803678	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803679	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803680	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7249827	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7249834	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250004	0.83[EUR][1000 genomes]
rs7250005	0.81[EUR][1000 genomes]
rs7250076	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250171	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251868	0.80[EUR][1000 genomes]
rs7508149	0.80[EUR][1000 genomes]
rs8101657	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104573	0.83[EUR][1000 genomes]
rs8105860	0.83[EUR][1000 genomes]
rs8113487	0.88[EUR][1000 genomes]
rs8113750	0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6509141	ZNF223	cis	Thyroid	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44600400-44616200	ZNF genes & repeats	Liver	Liver
2	chr19:44600800-44614000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:44600800-44614600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:44604800-44616000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:44605200-44614600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:44606600-44616400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:44608200-44613800	ZNF genes & repeats	Primary B cells from cord blood	blood
8	chr19:44608200-44614600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:44608200-44615800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:44608400-44614400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:44608400-44614600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr19:44608400-44616000	ZNF genes & repeats	Fetal Brain Female	brain
13	chr19:44608600-44613200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:44608600-44615800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr19:44609200-44613200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
16	chr19:44610200-44613200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:44610200-44614600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
18	chr19:44610400-44614600	ZNF genes & repeats	Fetal Brain Male	brain
19	chr19:44612000-44616200	Weak transcription	HepG2	liver
20	chr19:44612200-44616000	Weak transcription	Fetal Thymus	thymus
21	chr19:44612400-44613200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:44612400-44614800	Weak transcription	Fetal Intestine Large	intestine
23	chr19:44612400-44615200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:44612400-44616000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:44612400-44616000	Weak transcription	Pancreas	Pancrea
26	chr19:44612400-44616200	Weak transcription	Gastric	stomach
27	chr19:44612400-44616400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:44612600-44614000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:44612600-44614400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:44612600-44615600	Weak transcription	HSMMtube	muscle
31	chr19:44612600-44615800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:44612600-44616000	Weak transcription	Placenta	Placenta
33	chr19:44612800-44613600	Weak transcription	Dnd41	blood
34	chr19:44612800-44614400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:44612800-44615400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:44612800-44615600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:44612800-44615600	Weak transcription	NHDF-Ad	bronchial
38	chr19:44612800-44615800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:44612800-44615800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:44612800-44615800	Weak transcription	NHEK	skin
41	chr19:44612800-44615800	Weak transcription	Osteobl	bone
42	chr19:44612800-44616000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:44612800-44616000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr19:44612800-44616200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:44612800-44616200	Weak transcription	Ovary	ovary
46	chr19:44612800-44616200	Weak transcription	Thymus	Thymus
47	chr19:44612800-44617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:44613000-44613200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:44613000-44613600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:44613000-44613800	Weak transcription	HSMM	muscle

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