Variant report

Variant	rs73546789
Chromosome Location	chr19:21687603-21687604
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	RFX5	chr19:21687564-21689643	IMR90	lung:	n/a	chr19:21688315-21688324 chr19:21688312-21688327 chr19:21688373-21688382
2	RFX5	chr19:21687129-21689681	SK-N-SH	brain:	n/a	chr19:21688315-21688324 chr19:21688312-21688327 chr19:21688373-21688382
3	MXI1	chr19:21687519-21689374	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr19:21687589-21687634	LNCaP	prostate:	n/a	n/a

Variant related genes	Relation type
ZNF429	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs4462729	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4462730	1.00[AMR][1000 genomes]
rs56217825	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59543267	1.00[AMR][1000 genomes]
rs60083403	1.00[AMR][1000 genomes]
rs61115928	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61663351	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7254975	1.00[AMR][1000 genomes]
rs7255176	1.00[AMR][1000 genomes]
rs7257308	1.00[AMR][1000 genomes]
rs7259339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546766	0.95[AFR][1000 genomes]
rs73546769	0.95[AFR][1000 genomes]
rs73546778	0.98[AFR][1000 genomes]
rs73546782	1.00[AFR][1000 genomes]
rs73546785	1.00[AFR][1000 genomes]
rs73546787	1.00[AFR][1000 genomes]
rs73548606	1.00[AMR][1000 genomes]
rs73548618	1.00[AMR][1000 genomes]
rs73548628	1.00[AMR][1000 genomes]
rs73926349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8107706	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv543941	chr19:21676223-21693215	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21658200-21687800	Weak transcription	Brain Substantia Nigra	brain
2	chr19:21673400-21687800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:21674800-21687800	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:21676000-21688000	Weak transcription	Fetal Stomach	stomach
5	chr19:21678000-21688000	Weak transcription	Thymus	Thymus
6	chr19:21679200-21688200	Weak transcription	Brain Angular Gyrus	brain
7	chr19:21680000-21687800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:21680000-21688200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:21680200-21688200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:21681200-21688400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:21681400-21688200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr19:21681600-21688200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:21681800-21688000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:21681800-21688000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:21681800-21688200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:21681800-21688400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:21683800-21688000	Weak transcription	Fetal Intestine Large	intestine
18	chr19:21687200-21687800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr19:21687200-21688200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:21687200-21688200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr19:21687200-21688200	Enhancers	Primary T cells from cord blood	blood
22	chr19:21687200-21688200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr19:21687400-21688000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr19:21687400-21688000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr19:21687400-21688000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:21687400-21688000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr19:21687400-21688000	Enhancers	Dnd41	blood
28	chr19:21687400-21688200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:21687400-21688200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:21687600-21687800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:21687600-21687800	Enhancers	Fetal Heart	heart
32	chr19:21687600-21688000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:21687600-21688000	Enhancers	Brain Anterior Caudate	brain
34	chr19:21687600-21688000	Enhancers	Brain Cingulate Gyrus	brain
35	chr19:21687600-21688000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr19:21687600-21688000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr19:21687600-21688000	Enhancers	K562	blood
38	chr19:21687600-21688000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr19:21687600-21688200	Enhancers	Primary B cells from peripheral blood	blood
40	chr19:21687600-21688200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr19:21687600-21688200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr19:21687600-21688200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr19:21687600-21688200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:21687600-21688200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:21687600-21688200	Enhancers	Liver	Liver
46	chr19:21687600-21688200	Enhancers	Duodenum Mucosa	Duodenum
47	chr19:21687600-21688200	Enhancers	Fetal Lung	lung
48	chr19:21687600-21689400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:21687600-21689600	Active TSS	Brain Germinal Matrix	brain

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