Variant report

Variant	rs11879143
Chromosome Location	chr19:55853497-55853498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55850320-55853763	K562	blood:	n/a	n/a
2	POLR2A	chr19:55849929-55853529	K562	blood:	n/a	n/a
3	ZBTB7A	chr19:55853326-55853880	K562	blood:	n/a	chr19:55853851-55853859

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55851487..55853796-chr19:55888849..55891400,2	MCF-7	breast:
2	chr19:55720239..55723202-chr19:55851102..55853910,2	MCF-7	breast:
3	chr19:55848515..55857343-chr19:55894079..55900232,19	MCF-7	breast:
4	chr19:55853165..55857260-chr19:55879821..55883048,3	MCF-7	breast:
5	chr19:55847527..55853936-chr19:55895162..55898950,13	K562	blood:
6	chr19:55849530..55854944-chr19:55915448..55920939,7	K562	blood:
7	chr19:55851377..55854272-chr19:55873809..55875979,2	MCF-7	breast:
8	chr19:55848915..55854876-chr19:55892600..55899757,13	MCF-7	breast:
9	chr19:55847613..55856135-chr19:55893756..55900268,15	K562	blood:

No data

Variant related genes	Relation type
SUV420H2	TF binding region
ENSG00000233493	Chromatin interaction
ENSG00000269275	Chromatin interaction
ENSG00000095752	Chromatin interaction
ENSG00000180043	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10416488	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10416740	1.00[EUR][1000 genomes]
rs1058511	0.86[YRI][hapmap]
rs12609926	1.00[EUR][1000 genomes]
rs58051372	0.98[EUR][1000 genomes]
rs59262883	0.96[EUR][1000 genomes]
rs59493644	0.95[EUR][1000 genomes]
rs59695872	0.96[EUR][1000 genomes]
rs59944279	1.00[EUR][1000 genomes]
rs73605199	0.95[EUR][1000 genomes]
rs73605200	0.95[EUR][1000 genomes]
rs73605202	0.96[EUR][1000 genomes]
rs73607003	0.98[EUR][1000 genomes]
rs73607005	0.98[EUR][1000 genomes]
rs73607008	0.98[EUR][1000 genomes]
rs73607019	1.00[EUR][1000 genomes]
rs73607024	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
7	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv912461	chr19:55845386-55897327	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
9	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
11	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
12	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
13	esv1799638	chr19:55850652-55883879	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55852000-55853800	Enhancers	Fetal Brain Male	brain
2	chr19:55852200-55853600	Enhancers	Fetal Heart	heart
3	chr19:55852400-55860200	Weak transcription	Aorta	Aorta
4	chr19:55852600-55854800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:55852600-55857000	Weak transcription	Stomach Mucosa	stomach
6	chr19:55852600-55857400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:55852800-55854000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:55852800-55857400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:55852800-55859600	Weak transcription	Psoas Muscle	Psoas
10	chr19:55853000-55853600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
11	chr19:55853000-55853600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr19:55853000-55853600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:55853000-55853800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:55853000-55855200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:55853200-55853600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:55853200-55853600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:55853200-55853600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
18	chr19:55853200-55853600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
19	chr19:55853200-55853600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:55853200-55853600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:55853200-55853600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:55853200-55853600	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
23	chr19:55853200-55853600	Weak transcription	Brain Substantia Nigra	brain
24	chr19:55853200-55853600	Genic enhancers	Placenta	Placenta
25	chr19:55853200-55853600	Genic enhancers	Gastric	stomach
26	chr19:55853200-55853600	Genic enhancers	Spleen	Spleen
27	chr19:55853200-55853600	Enhancers	HMEC	breast
28	chr19:55853200-55853600	Enhancers	HSMMtube	muscle
29	chr19:55853200-55853800	Genic enhancers	H1 Cell Line	embryonic stem cell
30	chr19:55853200-55853800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:55853200-55853800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:55853200-55853800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr19:55853200-55853800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr19:55853200-55853800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:55853200-55853800	Weak transcription	Liver	Liver
36	chr19:55853200-55853800	Genic enhancers	Ovary	ovary
37	chr19:55853200-55853800	Genic enhancers	Right Ventricle	heart
38	chr19:55853200-55854000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:55853200-55854000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:55853200-55854000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:55853200-55854000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr19:55853200-55854200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:55853200-55854200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr19:55853200-55854200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:55853200-55854200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:55853200-55854200	Genic enhancers	A549	lung
47	chr19:55853200-55854600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr19:55853200-55854800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:55853200-55855000	Weak transcription	Primary T cells from cord blood	blood
50	chr19:55853200-55855200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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