Variant report

Variant	rs324095
Chromosome Location	chr19:52956289-52956290
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	MXI1	chr19:52956236-52957611	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr19:52954835-52956396	K562	blood:	n/a	n/a
3	CTCF	chr19:52956220-52956370	WI-38	lung:	n/a	n/a

Variant related genes	Relation type
ZNF578	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1112889	0.87[AFR][1000 genomes]
rs1115659	0.88[AFR][1000 genomes]
rs1115660	0.87[AFR][1000 genomes]
rs12459176	0.89[AFR][1000 genomes]
rs12460429	0.89[AFR][1000 genomes]
rs1428177	0.88[AFR][1000 genomes]
rs1457854	0.89[AFR][1000 genomes]
rs1457855	0.89[AFR][1000 genomes]
rs1457856	0.89[AFR][1000 genomes]
rs1457857	0.85[AFR][1000 genomes]
rs1599602	1.00[EUR][1000 genomes]
rs1817266	0.86[AFR][1000 genomes]
rs1840997	0.88[AFR][1000 genomes]
rs1840998	0.88[AFR][1000 genomes]
rs1864019	0.88[AFR][1000 genomes]
rs2115101	0.89[AFR][1000 genomes]
rs2168792	0.89[AFR][1000 genomes]
rs2903895	0.86[AFR][1000 genomes]
rs324093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324102	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324105	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs326450	1.00[EUR][1000 genomes]
rs35170850	0.88[AFR][1000 genomes]
rs4802949	0.88[AFR][1000 genomes]
rs4802950	0.84[AFR][1000 genomes]
rs59465772	1.00[EUR][1000 genomes]
rs60186879	1.00[EUR][1000 genomes]
rs60952057	1.00[EUR][1000 genomes]
rs61039331	1.00[EUR][1000 genomes]
rs6509641	0.86[AFR][1000 genomes]
rs6509643	0.90[AFR][1000 genomes]
rs7252655	0.88[AFR][1000 genomes]
rs8101762	1.00[EUR][1000 genomes]
rs8110920	0.86[AFR][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	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3415774	chr19:52938189-52970794	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52953600-52956400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:52954000-52956400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:52954000-52961600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr19:52954400-52961400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr19:52954400-52962600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:52954600-52956600	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr19:52954600-52956800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:52954800-52956400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:52954800-52956600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:52955000-52956600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:52955200-52956400	Weak transcription	Stomach Mucosa	stomach
12	chr19:52955600-52957800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
13	chr19:52955800-52957800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr19:52955800-52958200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr19:52955800-52961400	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr19:52956000-52956400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
17	chr19:52956000-52956600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
18	chr19:52956000-52957000	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr19:52956000-52957200	Active TSS	Brain Anterior Caudate	brain
20	chr19:52956000-52957600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:52956000-52958000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr19:52956000-52969600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:52956000-52986200	ZNF genes & repeats	Liver	Liver
24	chr19:52956200-52956400	ZNF genes & repeats	Primary T cells from cord blood	blood
25	chr19:52956200-52956400	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr19:52956200-52956400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
27	chr19:52956200-52956400	ZNF genes & repeats	Right Atrium	heart
28	chr19:52956200-52956400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
29	chr19:52956200-52956400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
30	chr19:52956200-52956600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
31	chr19:52956200-52957000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:52956200-52957000	Active TSS	Brain Angular Gyrus	brain
33	chr19:52956200-52957200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:52956200-52957200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:52956200-52957200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
36	chr19:52956200-52957200	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr19:52956200-52957200	Active TSS	Fetal Heart	heart
38	chr19:52956200-52957200	Active TSS	Right Ventricle	heart
39	chr19:52956200-52957400	Active TSS	Fetal Brain Male	brain
40	chr19:52956200-52957600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:52956200-52957600	Active TSS	Fetal Kidney	kidney
42	chr19:52956200-52957600	ZNF genes & repeats	NHEK	skin
43	chr19:52956200-52957800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:52956200-52958000	Active TSS	NHDF-Ad	bronchial
45	chr19:52956200-52958200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
46	chr19:52956200-52958400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:52956200-52958400	Active TSS	Psoas Muscle	Psoas
48	chr19:52956200-52961400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr19:52956200-52961400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:52956200-52961600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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